[med-svn] [jaligner] 01/01: Imported Upstream version 1.0
Timothy Booth
tbooth-guest at moszumanska.debian.org
Sun Feb 1 18:50:58 UTC 2015
This is an automated email from the git hooks/post-receive script.
tbooth-guest pushed a commit to branch master
in repository jaligner.
commit fc41bfe1e51b2429ca0bf04073c8b5347de748a2
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Sun Feb 1 18:50:09 2015 +0000
Imported Upstream version 1.0
---
LICENSE | 285 ++++
README | 3 +
api/allclasses-frame.html | 110 ++
api/allclasses-noframe.html | 110 ++
api/constant-values.html | 298 ++++
api/deprecated-list.html | 134 ++
api/help-doc.html | 193 +++
api/index-all.html | 798 ++++++++++
api/index.html | 26 +
api/jaligner.css | 38 +
api/jaligner/Alignment.html | 891 +++++++++++
api/jaligner/Cell.html | 385 +++++
api/jaligner/Directions.html | 321 ++++
api/jaligner/Markups.html | 321 ++++
api/jaligner/Sequence.html | 635 ++++++++
api/jaligner/SmithWatermanGotoh.html | 247 +++
api/jaligner/class-use/Alignment.html | 229 +++
api/jaligner/class-use/Cell.html | 136 ++
api/jaligner/class-use/Directions.html | 136 ++
api/jaligner/class-use/Markups.html | 136 ++
api/jaligner/class-use/Sequence.html | 242 +++
api/jaligner/class-use/SmithWatermanGotoh.html | 136 ++
api/jaligner/example/Example.html | 307 ++++
api/jaligner/example/class-use/Example.html | 136 ++
api/jaligner/example/package-frame.html | 32 +
api/jaligner/example/package-summary.html | 168 ++
api/jaligner/example/package-tree.html | 145 ++
api/jaligner/example/package-use.html | 136 ++
api/jaligner/formats/CLUSTAL.html | 322 ++++
api/jaligner/formats/FASTA.html | 302 ++++
api/jaligner/formats/Format.html | 309 ++++
api/jaligner/formats/FormatFactory.html | 301 ++++
api/jaligner/formats/Pair.html | 278 ++++
api/jaligner/formats/class-use/CLUSTAL.html | 136 ++
api/jaligner/formats/class-use/FASTA.html | 136 ++
api/jaligner/formats/class-use/Format.html | 220 +++
api/jaligner/formats/class-use/FormatFactory.html | 172 ++
api/jaligner/formats/class-use/Pair.html | 136 ++
api/jaligner/formats/package-frame.html | 40 +
api/jaligner/formats/package-summary.html | 183 +++
api/jaligner/formats/package-tree.html | 147 ++
api/jaligner/formats/package-use.html | 168 ++
api/jaligner/matrix/MatricesCompartor.html | 277 ++++
api/jaligner/matrix/Matrix.html | 317 ++++
api/jaligner/matrix/MatrixLoader.html | 342 ++++
api/jaligner/matrix/MatrixLoaderException.html | 238 +++
.../matrix/class-use/MatricesCompartor.html | 136 ++
api/jaligner/matrix/class-use/Matrix.html | 237 +++
api/jaligner/matrix/class-use/MatrixLoader.html | 136 ++
.../matrix/class-use/MatrixLoaderException.html | 196 +++
api/jaligner/matrix/package-frame.html | 47 +
api/jaligner/matrix/package-summary.html | 189 +++
api/jaligner/matrix/package-tree.html | 152 ++
api/jaligner/matrix/package-use.html | 187 +++
api/jaligner/package-frame.html | 42 +
api/jaligner/package-summary.html | 188 +++
api/jaligner/package-tree.html | 146 ++
api/jaligner/package-use.html | 212 +++
api/jaligner/test/AlignmentScoreChecker.html | 260 +++
api/jaligner/test/RandomSequenceGenerator.html | 284 ++++
.../test/class-use/AlignmentScoreChecker.html | 136 ++
.../test/class-use/RandomSequenceGenerator.html | 136 ++
api/jaligner/test/package-frame.html | 34 +
api/jaligner/test/package-summary.html | 171 ++
api/jaligner/test/package-tree.html | 145 ++
api/jaligner/test/package-use.html | 136 ++
api/jaligner/ui/AlignCommandLine.html | 260 +++
api/jaligner/ui/AlignWindow.html | 569 +++++++
api/jaligner/ui/class-use/AlignCommandLine.html | 136 ++
api/jaligner/ui/class-use/AlignWindow.html | 136 ++
api/jaligner/ui/clipboard/ClipboardHandler.html | 248 +++
api/jaligner/ui/clipboard/ClipboardHandlerAWT.html | 293 ++++
.../ui/clipboard/ClipboardHandlerFactory.html | 236 +++
.../ui/clipboard/ClipboardHandlerJNLP.html | 293 ++++
api/jaligner/ui/clipboard/ClipboardListener.html | 225 +++
api/jaligner/ui/clipboard/ClipboardPoller.html | 314 ++++
.../ui/clipboard/class-use/ClipboardHandler.html | 196 +++
.../clipboard/class-use/ClipboardHandlerAWT.html | 136 ++
.../class-use/ClipboardHandlerFactory.html | 136 ++
.../clipboard/class-use/ClipboardHandlerJNLP.html | 136 ++
.../ui/clipboard/class-use/ClipboardListener.html | 199 +++
.../ui/clipboard/class-use/ClipboardPoller.html | 136 ++
api/jaligner/ui/clipboard/package-frame.html | 51 +
api/jaligner/ui/clipboard/package-summary.html | 198 +++
api/jaligner/ui/clipboard/package-tree.html | 155 ++
api/jaligner/ui/clipboard/package-use.html | 188 +++
api/jaligner/ui/filechooser/FileChooser.html | 372 +++++
.../ui/filechooser/FileChooserException.html | 242 +++
.../ui/filechooser/FileChooserFactory.html | 236 +++
api/jaligner/ui/filechooser/FileChooserJNLP.html | 325 ++++
.../ui/filechooser/FileChooserTrusted.html | 325 ++++
api/jaligner/ui/filechooser/NamedInputStream.html | 288 ++++
.../ui/filechooser/class-use/FileChooser.html | 196 +++
.../class-use/FileChooserException.html | 215 +++
.../filechooser/class-use/FileChooserFactory.html | 136 ++
.../ui/filechooser/class-use/FileChooserJNLP.html | 136 ++
.../filechooser/class-use/FileChooserTrusted.html | 136 ++
.../ui/filechooser/class-use/NamedInputStream.html | 217 +++
api/jaligner/ui/filechooser/package-frame.html | 51 +
api/jaligner/ui/filechooser/package-summary.html | 197 +++
api/jaligner/ui/filechooser/package-tree.html | 153 ++
api/jaligner/ui/filechooser/package-use.html | 193 +++
api/jaligner/ui/images/ToolbarIcons.html | 441 +++++
api/jaligner/ui/images/class-use/ToolbarIcons.html | 136 ++
api/jaligner/ui/images/package-frame.html | 32 +
api/jaligner/ui/images/package-summary.html | 167 ++
api/jaligner/ui/images/package-tree.html | 145 ++
api/jaligner/ui/images/package-use.html | 136 ++
api/jaligner/ui/logging/DocumentHandler.html | 310 ++++
api/jaligner/ui/logging/RecordFormatter.html | 318 ++++
.../ui/logging/class-use/DocumentHandler.html | 136 ++
.../ui/logging/class-use/RecordFormatter.html | 136 ++
api/jaligner/ui/logging/package-frame.html | 34 +
api/jaligner/ui/logging/package-summary.html | 171 ++
api/jaligner/ui/logging/package-tree.html | 149 ++
api/jaligner/ui/logging/package-use.html | 136 ++
api/jaligner/ui/package-frame.html | 34 +
api/jaligner/ui/package-summary.html | 171 ++
api/jaligner/ui/package-tree.html | 160 ++
api/jaligner/ui/package-use.html | 136 ++
api/jaligner/ui/util/PrintJobMointor.html | 235 +++
api/jaligner/ui/util/TextComponentUtil.html | 449 ++++++
.../ui/util/TextComponentUtilException.html | 238 +++
.../ui/util/class-use/PrintJobMointor.html | 136 ++
.../ui/util/class-use/TextComponentUtil.html | 136 ++
.../util/class-use/TextComponentUtilException.html | 197 +++
api/jaligner/ui/util/package-frame.html | 45 +
api/jaligner/ui/util/package-summary.html | 185 +++
api/jaligner/ui/util/package-tree.html | 150 ++
api/jaligner/ui/util/package-use.html | 162 ++
api/jaligner/util/Commons.html | 394 +++++
api/jaligner/util/SequenceParser.html | 297 ++++
api/jaligner/util/SequenceParserException.html | 238 +++
api/jaligner/util/class-use/Commons.html | 136 ++
api/jaligner/util/class-use/SequenceParser.html | 136 ++
.../util/class-use/SequenceParserException.html | 180 +++
api/jaligner/util/package-frame.html | 45 +
api/jaligner/util/package-summary.html | 185 +++
api/jaligner/util/package-tree.html | 150 ++
api/jaligner/util/package-use.html | 162 ++
api/overview-frame.html | 64 +
api/overview-summary.html | 193 +++
api/overview-tree.html | 186 +++
api/package-list | 12 +
api/packages.html | 37 +
api/resources/inherit.gif | Bin 0 -> 57 bytes
api/serialized-form.html | 1232 ++++++++++++++
build.properties | 34 +
build.xml | 64 +
jaligner.bat | 1 +
jaligner.css | 38 +
jaligner.jar | Bin 0 -> 164489 bytes
jaligner.sh | 1 +
src/NAligner/.cvsignore | 13 +
src/NAligner/Alignment.cs | 244 +++
src/NAligner/AssemblyInfo.cs | 79 +
src/NAligner/Cell.cs | 75 +
src/NAligner/Directions.cs | 38 +
src/NAligner/Markups.cs | 39 +
src/NAligner/Matrix.cs | 117 ++
src/NAligner/NAligner.csproj | 189 +++
src/NAligner/NAligner.ndoc | 296 ++++
src/NAligner/NamespaceDoc.cs | 36 +
src/NAligner/Sequence.cs | 283 ++++
src/NAligner/SmithWatermanGotoh.cs | 416 +++++
src/NAligner/formats/AlignmentFormatter.cs | 44 +
src/NAligner/formats/CLUSTAL.cs | 117 ++
src/NAligner/formats/FASTA.cs | 70 +
src/NAligner/formats/FormatterFactory.cs | 72 +
src/NAligner/formats/NamespaceDoc.cs | 29 +
src/NAligner/formats/Pair.cs | 189 +++
src/NAligner/matrices/BLOSUM100 | 31 +
src/NAligner/matrices/BLOSUM30 | 31 +
src/NAligner/matrices/BLOSUM35 | 31 +
src/NAligner/matrices/BLOSUM40 | 31 +
src/NAligner/matrices/BLOSUM45 | 31 +
src/NAligner/matrices/BLOSUM50 | 31 +
src/NAligner/matrices/BLOSUM55 | 31 +
src/NAligner/matrices/BLOSUM60 | 31 +
src/NAligner/matrices/BLOSUM62 | 31 +
src/NAligner/matrices/BLOSUM65 | 31 +
src/NAligner/matrices/BLOSUM70 | 31 +
src/NAligner/matrices/BLOSUM75 | 31 +
src/NAligner/matrices/BLOSUM80 | 31 +
src/NAligner/matrices/BLOSUM85 | 31 +
src/NAligner/matrices/BLOSUM90 | 31 +
src/NAligner/matrices/BLOSUMN | 31 +
src/NAligner/matrices/DAYHOFF | 32 +
src/NAligner/matrices/EDNAFULL | 25 +
src/NAligner/matrices/GONNET | 26 +
src/NAligner/matrices/IDENTITY | 25 +
src/NAligner/matrices/MATCH | 25 +
src/NAligner/matrices/PAM10 | 34 +
src/NAligner/matrices/PAM100 | 34 +
src/NAligner/matrices/PAM110 | 34 +
src/NAligner/matrices/PAM120 | 34 +
src/NAligner/matrices/PAM130 | 34 +
src/NAligner/matrices/PAM140 | 34 +
src/NAligner/matrices/PAM150 | 34 +
src/NAligner/matrices/PAM160 | 34 +
src/NAligner/matrices/PAM170 | 34 +
src/NAligner/matrices/PAM180 | 34 +
src/NAligner/matrices/PAM190 | 34 +
src/NAligner/matrices/PAM20 | 34 +
src/NAligner/matrices/PAM200 | 34 +
src/NAligner/matrices/PAM210 | 34 +
src/NAligner/matrices/PAM220 | 34 +
src/NAligner/matrices/PAM230 | 34 +
src/NAligner/matrices/PAM240 | 34 +
src/NAligner/matrices/PAM250 | 34 +
src/NAligner/matrices/PAM260 | 34 +
src/NAligner/matrices/PAM270 | 34 +
src/NAligner/matrices/PAM280 | 34 +
src/NAligner/matrices/PAM290 | 34 +
src/NAligner/matrices/PAM30 | 34 +
src/NAligner/matrices/PAM300 | 34 +
src/NAligner/matrices/PAM310 | 34 +
src/NAligner/matrices/PAM320 | 34 +
src/NAligner/matrices/PAM330 | 34 +
src/NAligner/matrices/PAM340 | 34 +
src/NAligner/matrices/PAM350 | 34 +
src/NAligner/matrices/PAM360 | 34 +
src/NAligner/matrices/PAM370 | 34 +
src/NAligner/matrices/PAM380 | 34 +
src/NAligner/matrices/PAM390 | 34 +
src/NAligner/matrices/PAM40 | 34 +
src/NAligner/matrices/PAM400 | 34 +
src/NAligner/matrices/PAM410 | 34 +
src/NAligner/matrices/PAM420 | 34 +
src/NAligner/matrices/PAM430 | 34 +
src/NAligner/matrices/PAM440 | 34 +
src/NAligner/matrices/PAM450 | 34 +
src/NAligner/matrices/PAM460 | 34 +
src/NAligner/matrices/PAM470 | 34 +
src/NAligner/matrices/PAM480 | 34 +
src/NAligner/matrices/PAM490 | 34 +
src/NAligner/matrices/PAM50 | 34 +
src/NAligner/matrices/PAM500 | 34 +
src/NAligner/matrices/PAM60 | 34 +
src/NAligner/matrices/PAM70 | 34 +
src/NAligner/matrices/PAM80 | 34 +
src/NAligner/matrices/PAM90 | 34 +
src/NAligner/matrices/TEST1 | 25 +
src/NAligner/naligner.sln | 21 +
src/NAligner/util/AlphanumericComparator.cs | 71 +
src/NAligner/util/Commons.cs | 115 ++
src/NAligner/util/NAlignerException.cs | 38 +
src/NAligner/util/Tokenizer.cs | 195 +++
src/jaligner/Alignment.java | 442 ++++++
src/jaligner/Cell.java | 98 ++
src/jaligner/Directions.java | 44 +
src/jaligner/Markups.java | 47 +
src/jaligner/Sequence.java | 195 +++
src/jaligner/SmithWatermanGotoh.java | 358 +++++
src/jaligner/example/Example.java | 112 ++
src/jaligner/example/package.html | 8 +
src/jaligner/example/sequences/p53_human.fasta | 7 +
src/jaligner/example/sequences/p53_mouse.fasta | 8 +
src/jaligner/formats/CLUSTAL.java | 121 ++
src/jaligner/formats/FASTA.java | 79 +
src/jaligner/formats/Format.java | 59 +
src/jaligner/formats/FormatFactory.java | 84 +
src/jaligner/formats/Pair.java | 191 +++
src/jaligner/formats/package.html | 8 +
src/jaligner/matrix/MatricesCompartor.java | 68 +
src/jaligner/matrix/Matrix.java | 73 +
src/jaligner/matrix/MatrixLoader.java | 220 +++
src/jaligner/matrix/MatrixLoaderException.java | 39 +
src/jaligner/matrix/matrices/BLOSUM100 | 31 +
src/jaligner/matrix/matrices/BLOSUM30 | 31 +
src/jaligner/matrix/matrices/BLOSUM35 | 31 +
src/jaligner/matrix/matrices/BLOSUM40 | 31 +
src/jaligner/matrix/matrices/BLOSUM45 | 31 +
src/jaligner/matrix/matrices/BLOSUM50 | 31 +
src/jaligner/matrix/matrices/BLOSUM55 | 31 +
src/jaligner/matrix/matrices/BLOSUM60 | 31 +
src/jaligner/matrix/matrices/BLOSUM62 | 31 +
src/jaligner/matrix/matrices/BLOSUM65 | 31 +
src/jaligner/matrix/matrices/BLOSUM70 | 31 +
src/jaligner/matrix/matrices/BLOSUM75 | 31 +
src/jaligner/matrix/matrices/BLOSUM80 | 31 +
src/jaligner/matrix/matrices/BLOSUM85 | 31 +
src/jaligner/matrix/matrices/BLOSUM90 | 31 +
src/jaligner/matrix/matrices/BLOSUMN | 31 +
src/jaligner/matrix/matrices/DAYHOFF | 32 +
src/jaligner/matrix/matrices/EDNAFULL | 25 +
src/jaligner/matrix/matrices/GONNET | 26 +
src/jaligner/matrix/matrices/IDENTITY | 25 +
src/jaligner/matrix/matrices/MATCH | 25 +
src/jaligner/matrix/matrices/PAM10 | 34 +
src/jaligner/matrix/matrices/PAM100 | 34 +
src/jaligner/matrix/matrices/PAM110 | 34 +
src/jaligner/matrix/matrices/PAM120 | 34 +
src/jaligner/matrix/matrices/PAM130 | 34 +
src/jaligner/matrix/matrices/PAM140 | 34 +
src/jaligner/matrix/matrices/PAM150 | 34 +
src/jaligner/matrix/matrices/PAM160 | 34 +
src/jaligner/matrix/matrices/PAM170 | 34 +
src/jaligner/matrix/matrices/PAM180 | 34 +
src/jaligner/matrix/matrices/PAM190 | 34 +
src/jaligner/matrix/matrices/PAM20 | 34 +
src/jaligner/matrix/matrices/PAM200 | 34 +
src/jaligner/matrix/matrices/PAM210 | 34 +
src/jaligner/matrix/matrices/PAM220 | 34 +
src/jaligner/matrix/matrices/PAM230 | 34 +
src/jaligner/matrix/matrices/PAM240 | 34 +
src/jaligner/matrix/matrices/PAM250 | 34 +
src/jaligner/matrix/matrices/PAM260 | 34 +
src/jaligner/matrix/matrices/PAM270 | 34 +
src/jaligner/matrix/matrices/PAM280 | 34 +
src/jaligner/matrix/matrices/PAM290 | 34 +
src/jaligner/matrix/matrices/PAM30 | 34 +
src/jaligner/matrix/matrices/PAM300 | 34 +
src/jaligner/matrix/matrices/PAM310 | 34 +
src/jaligner/matrix/matrices/PAM320 | 34 +
src/jaligner/matrix/matrices/PAM330 | 34 +
src/jaligner/matrix/matrices/PAM340 | 34 +
src/jaligner/matrix/matrices/PAM350 | 34 +
src/jaligner/matrix/matrices/PAM360 | 34 +
src/jaligner/matrix/matrices/PAM370 | 34 +
src/jaligner/matrix/matrices/PAM380 | 34 +
src/jaligner/matrix/matrices/PAM390 | 34 +
src/jaligner/matrix/matrices/PAM40 | 34 +
src/jaligner/matrix/matrices/PAM400 | 34 +
src/jaligner/matrix/matrices/PAM410 | 34 +
src/jaligner/matrix/matrices/PAM420 | 34 +
src/jaligner/matrix/matrices/PAM430 | 34 +
src/jaligner/matrix/matrices/PAM440 | 34 +
src/jaligner/matrix/matrices/PAM450 | 34 +
src/jaligner/matrix/matrices/PAM460 | 34 +
src/jaligner/matrix/matrices/PAM470 | 34 +
src/jaligner/matrix/matrices/PAM480 | 34 +
src/jaligner/matrix/matrices/PAM490 | 34 +
src/jaligner/matrix/matrices/PAM50 | 34 +
src/jaligner/matrix/matrices/PAM500 | 34 +
src/jaligner/matrix/matrices/PAM60 | 34 +
src/jaligner/matrix/matrices/PAM70 | 34 +
src/jaligner/matrix/matrices/PAM80 | 34 +
src/jaligner/matrix/matrices/PAM90 | 34 +
src/jaligner/matrix/package.html | 8 +
src/jaligner/package.html | 8 +
src/jaligner/test/AlignmentScoreChecker.java | 131 ++
src/jaligner/test/RandomSequenceGenerator.java | 75 +
src/jaligner/test/package.html | 8 +
src/jaligner/ui/AlignCommandLine.java | 93 ++
src/jaligner/ui/AlignWindow.form | 896 +++++++++++
src/jaligner/ui/AlignWindow.java | 1679 ++++++++++++++++++++
src/jaligner/ui/clipboard/ClipboardHandler.java | 42 +
src/jaligner/ui/clipboard/ClipboardHandlerAWT.java | 67 +
.../ui/clipboard/ClipboardHandlerFactory.java | 56 +
.../ui/clipboard/ClipboardHandlerJNLP.java | 71 +
src/jaligner/ui/clipboard/ClipboardListener.java | 35 +
src/jaligner/ui/clipboard/ClipboardPoller.java | 94 ++
src/jaligner/ui/clipboard/package.html | 8 +
src/jaligner/ui/filechooser/FileChooser.java | 73 +
.../ui/filechooser/FileChooserException.java | 40 +
.../ui/filechooser/FileChooserFactory.java | 56 +
src/jaligner/ui/filechooser/FileChooserJNLP.java | 85 +
.../ui/filechooser/FileChooserTrusted.java | 104 ++
src/jaligner/ui/filechooser/NamedInputStream.java | 67 +
src/jaligner/ui/filechooser/package.html | 8 +
src/jaligner/ui/images/ToolbarIcons.java | 79 +
src/jaligner/ui/images/gifs/about.gif | Bin 0 -> 644 bytes
src/jaligner/ui/images/gifs/close.gif | Bin 0 -> 254 bytes
src/jaligner/ui/images/gifs/copy.gif | Bin 0 -> 288 bytes
src/jaligner/ui/images/gifs/cut.gif | Bin 0 -> 652 bytes
src/jaligner/ui/images/gifs/delete.gif | Bin 0 -> 208 bytes
src/jaligner/ui/images/gifs/jaligner.gif | Bin 0 -> 117 bytes
src/jaligner/ui/images/gifs/open.gif | Bin 0 -> 228 bytes
src/jaligner/ui/images/gifs/paste.gif | Bin 0 -> 298 bytes
src/jaligner/ui/images/gifs/print.gif | Bin 0 -> 293 bytes
src/jaligner/ui/images/gifs/save.gif | Bin 0 -> 255 bytes
src/jaligner/ui/images/package.html | 8 +
src/jaligner/ui/logging/DocumentHandler.java | 118 ++
src/jaligner/ui/logging/RecordFormatter.java | 70 +
src/jaligner/ui/logging/package.html | 8 +
src/jaligner/ui/package.html | 8 +
src/jaligner/ui/util/PrintJobMointor.java | 89 ++
src/jaligner/ui/util/TextComponentUtil.java | 281 ++++
.../ui/util/TextComponentUtilException.java | 39 +
src/jaligner/ui/util/package.html | 8 +
src/jaligner/util/Commons.java | 217 +++
src/jaligner/util/SequenceParser.java | 215 +++
src/jaligner/util/SequenceParserException.java | 38 +
src/jaligner/util/package.html | 8 +
385 files changed, 44873 insertions(+)
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..ae3157a
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,285 @@
+GNU GENERAL PUBLIC LICENSE
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+59 Temple Place - Suite 330, Boston, MA 02111-1307, USA
+
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom
+to share and change it. By contrast, the GNU General Public License is
+intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
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+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on,
+we want its recipients to know that what they have is not the
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+
+Finally, any free program is threatened constantly by software
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+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION
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+
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+versions of the General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
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+"any later version", you have the option of following the terms and
+conditions either of that version or of any later version published by
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+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO
+WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE
+LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS
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+
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+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
+AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU
+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
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+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
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+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
diff --git a/README b/README
new file mode 100644
index 0000000..d6b7b97
--- /dev/null
+++ b/README
@@ -0,0 +1,3 @@
+JAligner <http://jaligner.sf.net> - By: Ahmed Moustafa <ahmed at users.sf.net>
+
+JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
diff --git a/api/allclasses-frame.html b/api/allclasses-frame.html
new file mode 100644
index 0000000..f2bc052
--- /dev/null
+++ b/api/allclasses-frame.html
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+All Classes (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameHeadingFont">
+<B>All Classes</B></FONT>
+<BR>
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui" target="classFrame">AlignCommandLine</A>
+<BR>
+<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui" target="classFrame">AlignWindow</A>
+<BR>
+<A HREF="jaligner/Alignment.html" title="class in jaligner" target="classFrame">Alignment</A>
+<BR>
+<A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test" target="classFrame">AlignmentScoreChecker</A>
+<BR>
+<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats" target="classFrame">CLUSTAL</A>
+<BR>
+<A HREF="jaligner/Cell.html" title="class in jaligner" target="classFrame">Cell</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard" target="classFrame"><I>ClipboardHandler</I></A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardHandlerAWT</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardHandlerFactory</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardHandlerJNLP</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard" target="classFrame"><I>ClipboardListener</I></A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardPoller</A>
+<BR>
+<A HREF="jaligner/util/Commons.html" title="class in jaligner.util" target="classFrame">Commons</A>
+<BR>
+<A HREF="jaligner/Directions.html" title="class in jaligner" target="classFrame">Directions</A>
+<BR>
+<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging" target="classFrame">DocumentHandler</A>
+<BR>
+<A HREF="jaligner/example/Example.html" title="class in jaligner.example" target="classFrame">Example</A>
+<BR>
+<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats" target="classFrame">FASTA</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooser</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserException</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserFactory</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserJNLP</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserTrusted</A>
+<BR>
+<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats" target="classFrame">Format</A>
+<BR>
+<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats" target="classFrame">FormatFactory</A>
+<BR>
+<A HREF="jaligner/Markups.html" title="class in jaligner" target="classFrame">Markups</A>
+<BR>
+<A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix" target="classFrame">MatricesCompartor</A>
+<BR>
+<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix" target="classFrame">Matrix</A>
+<BR>
+<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix" target="classFrame">MatrixLoader</A>
+<BR>
+<A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix" target="classFrame">MatrixLoaderException</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser" target="classFrame">NamedInputStream</A>
+<BR>
+<A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats" target="classFrame">Pair</A>
+<BR>
+<A HREF="jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util" target="classFrame">PrintJobMointor</A>
+<BR>
+<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test" target="classFrame">RandomSequenceGenerator</A>
+<BR>
+<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging" target="classFrame">RecordFormatter</A>
+<BR>
+<A HREF="jaligner/Sequence.html" title="class in jaligner" target="classFrame">Sequence</A>
+<BR>
+<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util" target="classFrame">SequenceParser</A>
+<BR>
+<A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util" target="classFrame">SequenceParserException</A>
+<BR>
+<A HREF="jaligner/SmithWatermanGotoh.html" title="class in jaligner" target="classFrame">SmithWatermanGotoh</A>
+<BR>
+<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util" target="classFrame">TextComponentUtil</A>
+<BR>
+<A HREF="jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util" target="classFrame">TextComponentUtilException</A>
+<BR>
+<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images" target="classFrame">ToolbarIcons</A>
+<BR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+</BODY>
+</HTML>
diff --git a/api/allclasses-noframe.html b/api/allclasses-noframe.html
new file mode 100644
index 0000000..2e31c1d
--- /dev/null
+++ b/api/allclasses-noframe.html
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+All Classes (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameHeadingFont">
+<B>All Classes</B></FONT>
+<BR>
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui">AlignCommandLine</A>
+<BR>
+<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<BR>
+<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<BR>
+<A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test">AlignmentScoreChecker</A>
+<BR>
+<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A>
+<BR>
+<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><I>ClipboardHandler</I></A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard">ClipboardHandlerFactory</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><I>ClipboardListener</I></A>
+<BR>
+<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard">ClipboardPoller</A>
+<BR>
+<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<BR>
+<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>
+<BR>
+<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A>
+<BR>
+<A HREF="jaligner/example/Example.html" title="class in jaligner.example">Example</A>
+<BR>
+<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser">FileChooserFactory</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A>
+<BR>
+<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats">Format</A>
+<BR>
+<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A>
+<BR>
+<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>
+<BR>
+<A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix">MatricesCompartor</A>
+<BR>
+<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A>
+<BR>
+<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>
+<BR>
+<A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A>
+<BR>
+<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A>
+<BR>
+<A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A>
+<BR>
+<A HREF="jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util">PrintJobMointor</A>
+<BR>
+<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test">RandomSequenceGenerator</A>
+<BR>
+<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A>
+<BR>
+<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<BR>
+<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util">SequenceParser</A>
+<BR>
+<A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A>
+<BR>
+<A HREF="jaligner/SmithWatermanGotoh.html" title="class in jaligner">SmithWatermanGotoh</A>
+<BR>
+<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<BR>
+<A HREF="jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A>
+<BR>
+<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<BR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+</BODY>
+</HTML>
diff --git a/api/constant-values.html b/api/constant-values.html
new file mode 100644
index 0000000..235765c
--- /dev/null
+++ b/api/constant-values.html
@@ -0,0 +1,298 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Constant Field Values (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Constant Field Values (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H1>
+Constant Field Values</H1>
+</CENTER>
+<HR SIZE="4" NOSHADE>
+<B>Contents</B><UL>
+<LI><A HREF="#jaligner">jaligner.*</A>
+</UL>
+
+<A NAME="jaligner"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD ALIGN="left"><FONT SIZE="+2">
+<B>jaligner.*</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="0" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Alignment.GAP"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final char</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Alignment.html#GAP">GAP</A></CODE></TD>
+<TD ALIGN="right"><CODE>45</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="0" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Directions.DIAGONAL"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final byte</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Directions.html#DIAGONAL">DIAGONAL</A></CODE></TD>
+<TD ALIGN="right"><CODE>2</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Directions.LEFT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final byte</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Directions.html#LEFT">LEFT</A></CODE></TD>
+<TD ALIGN="right"><CODE>1</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Directions.STOP"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final byte</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Directions.html#STOP">STOP</A></CODE></TD>
+<TD ALIGN="right"><CODE>0</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Directions.UP"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final byte</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Directions.html#UP">UP</A></CODE></TD>
+<TD ALIGN="right"><CODE>3</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="0" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Markups.GAP"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final char</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Markups.html#GAP">GAP</A></CODE></TD>
+<TD ALIGN="right"><CODE>32</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Markups.IDENTITY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final char</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Markups.html#IDENTITY">IDENTITY</A></CODE></TD>
+<TD ALIGN="right"><CODE>124</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Markups.MISMATCH"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final char</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Markups.html#MISMATCH">MISMATCH</A></CODE></TD>
+<TD ALIGN="right"><CODE>46</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Markups.SIMILARITY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final char</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Markups.html#SIMILARITY">SIMILARITY</A></CODE></TD>
+<TD ALIGN="right"><CODE>58</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="0" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Sequence.NUCLEIC"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Sequence.html#NUCLEIC">NUCLEIC</A></CODE></TD>
+<TD ALIGN="right"><CODE>0</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.Sequence.PROTEIN"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/Sequence.html#PROTEIN">PROTEIN</A></CODE></TD>
+<TD ALIGN="right"><CODE>1</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="0" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.ui.filechooser.FileChooser.BUFFER_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/ui/filechooser/FileChooser.html#BUFFER_SIZE">BUFFER_SIZE</A></CODE></TD>
+<TD ALIGN="right"><CODE>4096</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="0" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="jaligner.ui.images.ToolbarIcons.GIFS_HOME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="jaligner/ui/images/ToolbarIcons.html#GIFS_HOME">GIFS_HOME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"/jaligner/ui/images/gifs/"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/deprecated-list.html b/api/deprecated-list.html
new file mode 100644
index 0000000..90dba7a
--- /dev/null
+++ b/api/deprecated-list.html
@@ -0,0 +1,134 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Deprecated List (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Deprecated List (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="deprecated-list.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Deprecated API</B></H2>
+</CENTER>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="deprecated-list.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/help-doc.html b/api/help-doc.html
new file mode 100644
index 0000000..1c081ac
--- /dev/null
+++ b/api/help-doc.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+API Help (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="API Help (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <A HREF="help-doc.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H1>
+How This API Document Is Organized</H1>
+</CENTER>
+This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.<H3>
+Overview</H3>
+<BLOCKQUOTE>
+
+<P>
+The <A HREF="overview-summary.html">Overview</A> page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.</BLOCKQUOTE>
+<H3>
+Package</H3>
+<BLOCKQUOTE>
+
+<P>
+Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain four categories:<UL>
+<LI>Interfaces (italic)<LI>Classes<LI>Exceptions<LI>Errors</UL>
+</BLOCKQUOTE>
+<H3>
+Class/Interface</H3>
+<BLOCKQUOTE>
+
+<P>
+Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:<UL>
+<LI>Class inheritance diagram<LI>Direct Subclasses<LI>All Known Subinterfaces<LI>All Known Implementing Classes<LI>Class/interface declaration<LI>Class/interface description
+<P>
+<LI>Nested Class Summary<LI>Field Summary<LI>Constructor Summary<LI>Method Summary
+<P>
+<LI>Field Detail<LI>Constructor Detail<LI>Method Detail</UL>
+Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.</BLOCKQUOTE>
+<H3>
+Use</H3>
+<BLOCKQUOTE>
+Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.</ [...]
+<H3>
+Tree (Class Hierarchy)</H3>
+<BLOCKQUOTE>
+There is a <A HREF="overview-tree.html">Class Hierarchy</A> page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with <code>java.lang.Object</code>. The interfaces do not inherit from <code>java.lang.Object</code>.<UL>
+<LI>When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.<LI>When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.</UL>
+</BLOCKQUOTE>
+<H3>
+Deprecated API</H3>
+<BLOCKQUOTE>
+The <A HREF="deprecated-list.html">Deprecated API</A> page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.</BLOCKQUOTE>
+<H3>
+Index</H3>
+<BLOCKQUOTE>
+The <A HREF="index-all.html">Index</A> contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.</BLOCKQUOTE>
+<H3>
+Prev/Next</H3>
+These links take you to the next or previous class, interface, package, or related page.<H3>
+Frames/No Frames</H3>
+These links show and hide the HTML frames. All pages are available with or without frames.
+<P>
+<H3>
+Serialized Form</H3>
+Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.
+<P>
+<FONT SIZE="-1">
+<EM>
+This help file applies to API documentation generated using the standard doclet.</EM>
+</FONT>
+<BR>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="help-doc.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/index-all.html b/api/index-all.html
new file mode 100644
index 0000000..0dde66b
--- /dev/null
+++ b/api/index-all.html
@@ -0,0 +1,798 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Index (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Index (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="index-all.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_I_">I</A> <A HREF="#_J_">J</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_W_">W</A> <HR>
+<A NAME="_A_"><!-- --></A><H2>
+<B>A</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#ABOUT"><B>ABOUT</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>About icon
+<DT><A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><B>AlignCommandLine</B></A> - class jaligner.ui.<A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui">AlignCommandLine</A>.<DD>Command line interface for JAligner.<DT><A HREF="jaligner/ui/AlignCommandLine.html#AlignCommandLine()"><B>AlignCommandLine()</B></A> -
+Constructor for class jaligner.ui.<A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui">AlignCommandLine</A>
+<DD>
+<DT><A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><B>AlignWindow</B></A> - class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>.<DD>Graphical user inteface for JAligner.<DT><A HREF="jaligner/ui/AlignWindow.html#AlignWindow()"><B>AlignWindow()</B></A> -
+Constructor for class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>Constructor
+<DT><A HREF="jaligner/Alignment.html" title="class in jaligner"><B>Alignment</B></A> - class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>.<DD>Holds the output of a pairwise sequences alignment.<DT><A HREF="jaligner/Alignment.html#Alignment()"><B>Alignment()</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>Constructor for Alignment
+<DT><A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><B>AlignmentScoreChecker</B></A> - class jaligner.test.<A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test">AlignmentScoreChecker</A>.<DD>Testing the scores of the alignments of the SmithWaterman algorithm<DT><A HREF="jaligner/test/AlignmentScoreChecker.html#AlignmentScoreChecker()"><B>AlignmentScoreChecker()</B></A> -
+Constructor for class jaligner.test.<A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test">AlignmentScoreChecker</A>
+<DD>
+<DT><A HREF="jaligner/Sequence.html#acidAt(int)"><B>acidAt(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the acid at specific location in the sequence
+<DT><A HREF="jaligner/SmithWatermanGotoh.html#align(jaligner.Sequence, jaligner.Sequence, jaligner.matrix.Matrix, float, float)"><B>align(Sequence, Sequence, Matrix, float, float)</B></A> -
+Static method in class jaligner.<A HREF="jaligner/SmithWatermanGotoh.html" title="class in jaligner">SmithWatermanGotoh</A>
+<DD>Aligns two sequences by Smith-Waterman algorithm
+</DL>
+<HR>
+<A NAME="_B_"><!-- --></A><H2>
+<B>B</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/filechooser/FileChooser.html#BUFFER_SIZE"><B>BUFFER_SIZE</B></A> -
+Static variable in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<DD>Buffer size while reading from or write to a file (4 KB)
+</DL>
+<HR>
+<A NAME="_C_"><!-- --></A><H2>
+<B>C</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#CLOSE"><B>CLOSE</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Close icon
+<DT><A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><B>CLUSTAL</B></A> - class jaligner.formats.<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A>.<DD>CLUSTAL format.<DT><A HREF="jaligner/formats/CLUSTAL.html#CLUSTAL()"><B>CLUSTAL()</B></A> -
+Constructor for class jaligner.formats.<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A>
+<DD>Constructor
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#COPY"><B>COPY</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Copy icon
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#CUT"><B>CUT</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Cut icon
+<DT><A HREF="jaligner/Cell.html" title="class in jaligner"><B>Cell</B></A> - class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>.<DD>A cell in a similarity matrix, to hold row, column and score.<DT><A HREF="jaligner/Cell.html#Cell()"><B>Cell()</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>Constructor
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><B>ClipboardHandler</B></A> - interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A>.<DD>Abstract class to handle setting and getting "text" contents of
+ the system clipboard.<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerAWT</B></A> - class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A>.<DD>Sets and gets the contents of the system clipboard.<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html#ClipboardHandlerAWT()"><B>ClipboardHandlerAWT()</B></A> -
+Constructor for class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A>
+<DD>
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerFactory</B></A> - class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard">ClipboardHandlerFactory</A>.<DD>A factory for <A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.<DT><A HREF="jaligner/ui/clipboard/ClipboardHa [...]
+Constructor for class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A>
+<DD>
+<DT><A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><B>ClipboardListener</B></A> - interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A>.<DD>Listener interface to get notified with the clipboard contents.<DT><A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><B>ClipboardPoller</B></A> - class jaligner. [...]
+Constructor for class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard">ClipboardPoller</A>
+<DD>Constructor
+<DT><A HREF="jaligner/util/Commons.html" title="class in jaligner.util"><B>Commons</B></A> - class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>.<DD>Global constants/varilables/settings<DT><A HREF="jaligner/util/Commons.html#Commons()"><B>Commons()</B></A> -
+Constructor for class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#calculateScore()"><B>calculateScore()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>Calculate the score of the alignment, not using the score field (the
+ function only uses sequence1, sequence2, matrix and gap penalties).
+<DT><A HREF="jaligner/ui/AlignWindow.html#changedUpdate(javax.swing.event.DocumentEvent)"><B>changedUpdate(DocumentEvent)</B></A> -
+Method in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>Implements changedUpdate of <CODE>DocumentListener</CODE>
+<DT><A HREF="jaligner/Alignment.html#checkScore()"><B>checkScore()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>Check if the calculated score matches the field score.
+<DT><A HREF="jaligner/ui/AlignWindow.html#clipboardCheck(java.lang.String)"><B>clipboardCheck(String)</B></A> -
+Method in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>Implements the notify method of the interface <A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardListener</CODE></A>
+<DT><A HREF="jaligner/ui/clipboard/ClipboardListener.html#clipboardCheck(java.lang.String)"><B>clipboardCheck(String)</B></A> -
+Method in interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A>
+<DD>Notifies the listener with the current contents of the clipboard.
+<DT><A HREF="jaligner/ui/logging/DocumentHandler.html#close()"><B>close()</B></A> -
+Method in class jaligner.ui.logging.<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A>
+<DD>
+<DT><A HREF="jaligner/matrix/MatricesCompartor.html#compare(java.lang.Object, java.lang.Object)"><B>compare(Object, Object)</B></A> -
+Method in class jaligner.matrix.<A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix">MatricesCompartor</A>
+<DD>
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#copy(javax.swing.text.JTextComponent)"><B>copy(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Copies the selected text to the system clipboard.
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#cut(javax.swing.text.JTextComponent)"><B>cut(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Copies the selected text to the system clipboad and then deletes it from
+ the text component.
+</DL>
+<HR>
+<A NAME="_D_"><!-- --></A><H2>
+<B>D</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#DELETE"><B>DELETE</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Delete icon
+<DT><A HREF="jaligner/Directions.html#DIAGONAL"><B>DIAGONAL</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>
+<DD>Traceback direction diagonal
+<DT><A HREF="jaligner/Directions.html" title="class in jaligner"><B>Directions</B></A> - class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>.<DD>Traceback directions.<DT><A HREF="jaligner/Directions.html#Directions()"><B>Directions()</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>
+<DD>
+<DT><A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><B>DocumentHandler</B></A> - class jaligner.ui.logging.<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A>.<DD>Logging handler of <CODE>JTextPane</CODE>.<DT><A HREF="jaligner/ui/logging/DocumentHandler.html#DocumentHandler(javax.swing.JTextPane)"><B>DocumentHandler(JTextPane)</B></A> -
+Constructor for class jaligner.ui.logging.<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A>
+<DD>Constructor
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#delete(javax.swing.text.JTextComponent)"><B>delete(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Deletes the selected text in a text component.
+</DL>
+<HR>
+<A NAME="_E_"><!-- --></A><H2>
+<B>E</B></H2>
+<DL>
+<DT><A HREF="jaligner/example/Example.html" title="class in jaligner.example"><B>Example</B></A> - class jaligner.example.<A HREF="jaligner/example/Example.html" title="class in jaligner.example">Example</A>.<DD>Example of using JAligner API to align P53 human aganist
+ P53 mouse using Smith-Waterman-Gotoh algorithm.<DT><A HREF="jaligner/example/Example.html#Example()"><B>Example()</B></A> -
+Constructor for class jaligner.example.<A HREF="jaligner/example/Example.html" title="class in jaligner.example">Example</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_F_"><!-- --></A><H2>
+<B>F</B></H2>
+<DL>
+<DT><A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>FASTA</B></A> - class jaligner.formats.<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A>.<DD><a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.<DT><A HREF="jaligner/formats/FASTA.html#FASTA()"><B>FASTA()</B></A> -
+Constructor for class jaligner.formats.<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A>
+<DD>Constructor for FASTA.
+<DT><A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><B>FileChooser</B></A> - class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>.<DD>Opens and saves files.<DT><A HREF="jaligner/ui/filechooser/FileChooser.html#FileChooser()"><B>FileChooser()</B></A> -
+Constructor for class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<DD>
+<DT><A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser"><B>FileChooserException</B></A> - exception jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A>.<DD>File chooser exception<DT><A HREF="jaligner/ui/filechooser/FileChooserException.html#FileChooserException(java.lang.String)"><B>FileChooserException(String)</B></A> -
+Constructor for class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A>
+<DD>
+<DT><A HREF="jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>FileChooserFactory</B></A> - class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser">FileChooserFactory</A>.<DD>A factory for <A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.<DT><A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title=" [...]
+Constructor for class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A>
+<DD>
+<DT><A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>FileChooserTrusted</B></A> - class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A>.<DD>Opens and saves files.<DT><A HREF="jaligner/ui/filechooser/FileChooserTrusted.html#FileChooserTrusted()"><B>FileChooserTrusted()</B></A> -
+Constructor for class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A>
+<DD>
+<DT><A HREF="jaligner/formats/Format.html" title="class in jaligner.formats"><B>Format</B></A> - class jaligner.formats.<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats">Format</A>.<DD>Abstract format<DT><A HREF="jaligner/formats/Format.html#Format()"><B>Format()</B></A> -
+Constructor for class jaligner.formats.<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats">Format</A>
+<DD>
+<DT><A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>FormatFactory</B></A> - class jaligner.formats.<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A>.<DD>Formats factory.<DT><A HREF="jaligner/ui/logging/DocumentHandler.html#flush()"><B>flush()</B></A> -
+Method in class jaligner.ui.logging.<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A>
+<DD>
+<DT><A HREF="jaligner/formats/CLUSTAL.html#format(java.lang.String[], java.lang.String[])"><B>format(String[], String[])</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A>
+<DD>Returns CLUSTAL format
+<DT><A HREF="jaligner/formats/CLUSTAL.html#format(jaligner.Alignment)"><B>format(Alignment)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A>
+<DD>Returns CLUSTAL format of the alignment
+<DT><A HREF="jaligner/formats/FASTA.html#format(jaligner.Sequence)"><B>format(Sequence)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A>
+<DD>Returns the name, description and sequence combined in one string.
+<DT><A HREF="jaligner/formats/FASTA.html#format(jaligner.Alignment)"><B>format(Alignment)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A>
+<DD>
+<DT><A HREF="jaligner/formats/Format.html#format(jaligner.Alignment)"><B>format(Alignment)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats">Format</A>
+<DD>Formats alignment
+<DT><A HREF="jaligner/formats/Pair.html#format(jaligner.Alignment)"><B>format(Alignment)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A>
+<DD>Formats an alignment object to the Pair_FORMAT format
+<DT><A HREF="jaligner/ui/logging/RecordFormatter.html#format(java.util.logging.LogRecord)"><B>format(LogRecord)</B></A> -
+Method in class jaligner.ui.logging.<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A>
+<DD>This method is called for every log records
+</DL>
+<HR>
+<A NAME="_G_"><!-- --></A><H2>
+<B>G</B></H2>
+<DL>
+<DT><A HREF="jaligner/Alignment.html#GAP"><B>GAP</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>Gap character
+<DT><A HREF="jaligner/Markups.html#GAP"><B>GAP</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>
+<DD>Markup line gap character
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#GIFS_HOME"><B>GIFS_HOME</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Path to the gifs folder
+<DT><A HREF="jaligner/test/RandomSequenceGenerator.html#generate(int)"><B>generate(int)</B></A> -
+Static method in class jaligner.test.<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test">RandomSequenceGenerator</A>
+<DD>Returns random sequence
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html#getClipboardHandler()"><B>getClipboardHandler()</B></A> -
+Static method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard">ClipboardHandlerFactory</A>
+<DD>Returns an instance of a concrete <A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.
+<DT><A HREF="jaligner/Cell.html#getCol()"><B>getCol()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandler.html#getContents()"><B>getContents()</B></A> -
+Method in interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A>
+<DD>Returns the contents of the system of the clipboard
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html#getContents()"><B>getContents()</B></A> -
+Method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A>
+<DD>Gets the contents of the system clipboard
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html#getContents()"><B>getContents()</B></A> -
+Method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A>
+<DD>Gets the contents of the system clipboard
+<DT><A HREF="jaligner/util/Commons.html#getCurrentRelease()"><B>getCurrentRelease()</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Returns the current release version of JAligner
+<DT><A HREF="jaligner/Sequence.html#getDescription()"><B>getDescription()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the sequence description
+<DT><A HREF="jaligner/Alignment.html#getExtend()"><B>getExtend()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/ui/filechooser/FileChooserFactory.html#getFileChooser()"><B>getFileChooser()</B></A> -
+Static method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser">FileChooserFactory</A>
+<DD>Returns an instance of a concrete <A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.
+<DT><A HREF="jaligner/util/Commons.html#getFileSeparator()"><B>getFileSeparator()</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Returns system file separator.
+<DT><A HREF="jaligner/formats/FormatFactory.html#getFormat(java.lang.String)"><B>getFormat(String)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A>
+<DD>Returns an instance of <A HREF="jaligner/formats/Format.html" title="class in jaligner.formats"><CODE>Format</CODE></A>.
+<DT><A HREF="jaligner/formats/FormatFactory.html#getFormats()"><B>getFormats()</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A>
+<DD>Returns a list of registered formats
+<DT><A HREF="jaligner/Alignment.html#getGaps()"><B>getGaps()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/ui/logging/RecordFormatter.html#getHead(java.util.logging.Handler)"><B>getHead(Handler)</B></A> -
+Method in class jaligner.ui.logging.<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A>
+<DD>This method is called just after the handler using this
+ formatter is created
+<DT><A HREF="jaligner/Sequence.html#getId()"><B>getId()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the sequence id
+<DT><A HREF="jaligner/formats/Format.html#getId()"><B>getId()</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats">Format</A>
+<DD>Returns format id
+<DT><A HREF="jaligner/matrix/Matrix.html#getId()"><B>getId()</B></A> -
+Method in class jaligner.matrix.<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getIdentity()"><B>getIdentity()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/ui/filechooser/NamedInputStream.html#getInputStream()"><B>getInputStream()</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A>
+<DD>
+<DT><A HREF="jaligner/formats/FormatFactory.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class jaligner.formats.<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A>
+<DD>Returns an instance for <A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><CODE>FormatFactory</CODE></A>.
+<DT><A HREF="jaligner/util/Commons.html#getJAlignerInfo()"><B>getJAlignerInfo()</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Returns information about JAligner
+<DT><A HREF="jaligner/util/Commons.html#getLineSeparator()"><B>getLineSeparator()</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Returns system line separator.
+<DT><A HREF="jaligner/Alignment.html#getMarkupLine()"><B>getMarkupLine()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getMatrix()"><B>getMatrix()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/ui/filechooser/NamedInputStream.html#getName()"><B>getName()</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getName1()"><B>getName1()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getName2()"><B>getName2()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getOpen()"><B>getOpen()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Cell.html#getRow()"><B>getRow()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getScore()"><B>getScore()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Cell.html#getScore()"><B>getScore()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>
+<DT><A HREF="jaligner/matrix/Matrix.html#getScore(char, char)"><B>getScore(char, char)</B></A> -
+Method in class jaligner.matrix.<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A>
+<DD>
+<DT><A HREF="jaligner/matrix/Matrix.html#getScores()"><B>getScores()</B></A> -
+Method in class jaligner.matrix.<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A>
+<DD>
+<DT><A HREF="jaligner/Sequence.html#getSequence()"><B>getSequence()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the sequence string
+<DT><A HREF="jaligner/Alignment.html#getSequence1()"><B>getSequence1()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getSequence2()"><B>getSequence2()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getSimilarity()"><B>getSimilarity()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getStart1()"><B>getStart1()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getStart2()"><B>getStart2()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#getSummary()"><B>getSummary()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>Returns a summary for alignment
+<DT><A HREF="jaligner/ui/logging/RecordFormatter.html#getTail(java.util.logging.Handler)"><B>getTail(Handler)</B></A> -
+Method in class jaligner.ui.logging.<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A>
+<DD>This method is called just after the handler using this
+ formatter is closed
+<DT><A HREF="jaligner/Sequence.html#getType()"><B>getType()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the sequence type (nucleic or protein)
+<DT><A HREF="jaligner/ui/filechooser/FileChooser.html#getUserDirectory()"><B>getUserDirectory()</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<DD>Gets the current user working directory
+<DT><A HREF="jaligner/util/Commons.html#getUserDirectory()"><B>getUserDirectory()</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Returns user's current directory.
+</DL>
+<HR>
+<A NAME="_I_"><!-- --></A><H2>
+<B>I</B></H2>
+<DL>
+<DT><A HREF="jaligner/Markups.html#IDENTITY"><B>IDENTITY</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>
+<DD>Markup line identity character
+<DT><A HREF="jaligner/ui/AlignWindow.html#insertUpdate(javax.swing.event.DocumentEvent)"><B>insertUpdate(DocumentEvent)</B></A> -
+Method in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>Implements insertUpdate of <CODE>DocumentListener</CODE>
+<DT><A HREF="jaligner/util/Commons.html#isJnlp()"><B>isJnlp()</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Returns true if jnlp is enabled
+</DL>
+<HR>
+<A NAME="_J_"><!-- --></A><H2>
+<B>J</B></H2>
+<DL>
+<DT><A HREF="jaligner/package-summary.html"><B>jaligner</B></A> - package jaligner<DD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm<DT><A HREF="jaligner/example/package-summary.html"><B>jaligner.example</B></A> - package jaligner.example<DD>Example for using API of JAligner to perform pairwise sequence alignment.<DT><A HREF="jaligner/formats/package-summary.html"><B>jaligner.formats</B></A> - package jaligner.formats<DD>Group of formats for output alignments.<DT>< [...]
+<HR>
+<A NAME="_L_"><!-- --></A><H2>
+<B>L</B></H2>
+<DL>
+<DT><A HREF="jaligner/Directions.html#LEFT"><B>LEFT</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>
+<DD>Traceback direction left
+<DT><A HREF="jaligner/Sequence.html#length()"><B>length()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the length of the sequence
+<DT><A HREF="jaligner/matrix/MatrixLoader.html#list(boolean)"><B>list(boolean)</B></A> -
+Static method in class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>
+<DD>Returns a list of the scoring matrices in the matrices home directory
+<DT><A HREF="jaligner/matrix/MatrixLoader.html#list()"><B>list()</B></A> -
+Static method in class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>
+<DD>Returns a list of the scoring matrices in the matrices home directory
+<DT><A HREF="jaligner/matrix/MatrixLoader.html#load(java.lang.String)"><B>load(String)</B></A> -
+Static method in class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>
+<DD>Loads scoring matrix from Jar file or file system.
+<DT><A HREF="jaligner/matrix/MatrixLoader.html#load(jaligner.ui.filechooser.NamedInputStream)"><B>load(NamedInputStream)</B></A> -
+Static method in class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>
+<DD>Loads scoring matrix from <CODE>InputStream</CODE>
+<DT><A HREF="jaligner/example/Example.html#loadP53Human()"><B>loadP53Human()</B></A> -
+Static method in class jaligner.example.<A HREF="jaligner/example/Example.html" title="class in jaligner.example">Example</A>
+<DD>
+<DT><A HREF="jaligner/example/Example.html#loadP53Mouse()"><B>loadP53Mouse()</B></A> -
+Static method in class jaligner.example.<A HREF="jaligner/example/Example.html" title="class in jaligner.example">Example</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_M_"><!-- --></A><H2>
+<B>M</B></H2>
+<DL>
+<DT><A HREF="jaligner/Markups.html#MISMATCH"><B>MISMATCH</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>
+<DD>Markup line mismatch character
+<DT><A HREF="jaligner/Markups.html" title="class in jaligner"><B>Markups</B></A> - class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>.<DD>Markups line characters.<DT><A HREF="jaligner/Markups.html#Markups()"><B>Markups()</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>
+<DD>
+<DT><A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><B>MatricesCompartor</B></A> - class jaligner.matrix.<A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix">MatricesCompartor</A>.<DD>Comparator to sort the scoring matrices by their names.<DT><A HREF="jaligner/matrix/MatricesCompartor.html#MatricesCompartor()"><B>MatricesCompartor()</B></A> -
+Constructor for class jaligner.matrix.<A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix">MatricesCompartor</A>
+<DD>
+<DT><A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>Matrix</B></A> - class jaligner.matrix.<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A>.<DD>Scoring matrix.<DT><A HREF="jaligner/matrix/Matrix.html#Matrix(java.lang.String, float[][])"><B>Matrix(String, float[][])</B></A> -
+Constructor for class jaligner.matrix.<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A>
+<DD>
+<DT><A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><B>MatrixLoader</B></A> - class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>.<DD>Scoring matrices loader from a jar file or a file system.<DT><A HREF="jaligner/matrix/MatrixLoader.html#MatrixLoader()"><B>MatrixLoader()</B></A> -
+Constructor for class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A>
+<DD>
+<DT><A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix"><B>MatrixLoaderException</B></A> - exception jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A>.<DD> <DT><A HREF="jaligner/matrix/MatrixLoaderException.html#MatrixLoaderException(java.lang.String)"><B>MatrixLoaderException(String)</B></A> -
+Constructor for class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A>
+<DD>
+<DT><A HREF="jaligner/example/Example.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class jaligner.example.<A HREF="jaligner/example/Example.html" title="class in jaligner.example">Example</A>
+<DD>
+<DT><A HREF="jaligner/test/AlignmentScoreChecker.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class jaligner.test.<A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test">AlignmentScoreChecker</A>
+<DD>
+<DT><A HREF="jaligner/test/RandomSequenceGenerator.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class jaligner.test.<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test">RandomSequenceGenerator</A>
+<DD>Displays 10 random protein sequences with length 50.
+<DT><A HREF="jaligner/ui/AlignCommandLine.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class jaligner.ui.<A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui">AlignCommandLine</A>
+<DD>
+<DT><A HREF="jaligner/ui/AlignWindow.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_N_"><!-- --></A><H2>
+<B>N</B></H2>
+<DL>
+<DT><A HREF="jaligner/Sequence.html#NUCLEIC"><B>NUCLEIC</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Sequence type nucleic.
+<DT><A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><B>NamedInputStream</B></A> - class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A>.<DD> <DT><A HREF="jaligner/ui/filechooser/NamedInputStream.html#NamedInputStream(java.lang.String, java.io.InputStream)"><B>NamedInputStream(String, InputStream)</B></A> -
+Constructor for class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A>
+<DD>
+<DT><A HREF="jaligner/ui/AlignWindow.html#nextFocusAction"><B>nextFocusAction</B></A> -
+Variable in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_O_"><!-- --></A><H2>
+<B>O</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#OPEN"><B>OPEN</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Open icon
+<DT><A HREF="jaligner/ui/filechooser/FileChooser.html#open()"><B>open()</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<DD>Shows a dialog to select a file
+<DT><A HREF="jaligner/ui/filechooser/FileChooserJNLP.html#open()"><B>open()</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A>
+<DD>Shows a dialog to select a file.
+<DT><A HREF="jaligner/ui/filechooser/FileChooserTrusted.html#open()"><B>open()</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A>
+<DD>Shows a dialog to select a file.
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#open(javax.swing.text.JTextComponent)"><B>open(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Opens a file and puts the contents of the file in a text component.
+</DL>
+<HR>
+<A NAME="_P_"><!-- --></A><H2>
+<B>P</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#PASTE"><B>PASTE</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Paste icon
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#PRINT"><B>PRINT</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Print icon
+<DT><A HREF="jaligner/Sequence.html#PROTEIN"><B>PROTEIN</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Sequence type protein.
+<DT><A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats"><B>Pair</B></A> - class jaligner.formats.<A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A>.<DD><a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.<DT><A HREF="jaligner/formats/Pair.html#Pair()"><B>Pair()</B></A> -
+Constructor for class jaligner.formats.<A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A>
+<DD>Constructor
+<DT><A HREF="jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><B>PrintJobMointor</B></A> - class jaligner.ui.util.<A HREF="jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util">PrintJobMointor</A>.<DD>Mointor for print job.<DT><A HREF="jaligner/util/SequenceParser.html#parse(java.lang.String)"><B>parse(String)</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util">SequenceParser</A>
+<DD>Returns a parsed Sequence from a string.
+<DT><A HREF="jaligner/util/SequenceParser.html#parse(java.io.File)"><B>parse(File)</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util">SequenceParser</A>
+<DD>Returns a Sequence parsed and loaded from a file
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#paste(javax.swing.text.JTextComponent)"><B>paste(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Copies the text contents of the system clipboard to the text component.
+<DT><A HREF="jaligner/ui/AlignWindow.html#prevFocusAction"><B>prevFocusAction</B></A> -
+Variable in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#print(javax.swing.text.JTextComponent)"><B>print(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Prints the contents of a text component.
+<DT><A HREF="jaligner/ui/logging/DocumentHandler.html#publish(java.util.logging.LogRecord)"><B>publish(LogRecord)</B></A> -
+Method in class jaligner.ui.logging.<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_R_"><!-- --></A><H2>
+<B>R</B></H2>
+<DL>
+<DT><A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><B>RandomSequenceGenerator</B></A> - class jaligner.test.<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test">RandomSequenceGenerator</A>.<DD>This class contains a random generator for protein sequences.<DT><A HREF="jaligner/test/RandomSequenceGenerator.html#RandomSequenceGenerator()"><B>RandomSequenceGenerator()</B></A> -
+Constructor for class jaligner.test.<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test">RandomSequenceGenerator</A>
+<DD>
+<DT><A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><B>RecordFormatter</B></A> - class jaligner.ui.logging.<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A>.<DD>Logging record formatter<DT><A HREF="jaligner/ui/logging/RecordFormatter.html#RecordFormatter()"><B>RecordFormatter()</B></A> -
+Constructor for class jaligner.ui.logging.<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A>
+<DD>
+<DT><A HREF="jaligner/formats/FormatFactory.html#registerFormat(jaligner.formats.Format)"><B>registerFormat(Format)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A>
+<DD>Registers format.
+<DT><A HREF="jaligner/ui/AlignWindow.html#removeUpdate(javax.swing.event.DocumentEvent)"><B>removeUpdate(DocumentEvent)</B></A> -
+Method in class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A>
+<DD>Implements removeUpdate of <CODE>DocumentListener</CODE>
+<DT><A HREF="jaligner/ui/clipboard/ClipboardPoller.html#run()"><B>run()</B></A> -
+Method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard">ClipboardPoller</A>
+<DD>Runs the thread
+</DL>
+<HR>
+<A NAME="_S_"><!-- --></A><H2>
+<B>S</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#SAVE"><B>SAVE</B></A> -
+Static variable in class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>Save icon
+<DT><A HREF="jaligner/Markups.html#SIMILARITY"><B>SIMILARITY</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner">Markups</A>
+<DD>Markup line similarity character
+<DT><A HREF="jaligner/Directions.html#STOP"><B>STOP</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>
+<DD>Traceback direction stop
+<DT><A HREF="jaligner/Sequence.html" title="class in jaligner"><B>Sequence</B></A> - class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>.<DD>A basic (nucleic or protein) sequence.<DT><A HREF="jaligner/Sequence.html#Sequence()"><B>Sequence()</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Constructor
+<DT><A HREF="jaligner/Sequence.html#Sequence(java.lang.String)"><B>Sequence(String)</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Constructor
+<DT><A HREF="jaligner/Sequence.html#Sequence(java.lang.String, java.lang.String, java.lang.String, int)"><B>Sequence(String, String, String, int)</B></A> -
+Constructor for class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Constructor
+<DT><A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util"><B>SequenceParser</B></A> - class jaligner.util.<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util">SequenceParser</A>.<DD>SequenceParser to sequences from different formats.<DT><A HREF="jaligner/util/SequenceParser.html#SequenceParser()"><B>SequenceParser()</B></A> -
+Constructor for class jaligner.util.<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util">SequenceParser</A>
+<DD>
+<DT><A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util"><B>SequenceParserException</B></A> - exception jaligner.util.<A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A>.<DD> <DT><A HREF="jaligner/util/SequenceParserException.html#SequenceParserException(java.lang.String)"><B>SequenceParserException(String)</B></A> -
+Constructor for class jaligner.util.<A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A>
+<DD>
+<DT><A HREF="jaligner/SmithWatermanGotoh.html" title="class in jaligner"><B>SmithWatermanGotoh</B></A> - class jaligner.<A HREF="jaligner/SmithWatermanGotoh.html" title="class in jaligner">SmithWatermanGotoh</A>.<DD>An implementation of the Smith-Waterman algorithm with Gotoh's improvement
+ for biological local pairwise sequence alignment.<DT><A HREF="jaligner/ui/filechooser/FileChooser.html#save(java.io.InputStream, java.lang.String)"><B>save(InputStream, String)</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<DD>Saves an input stream to a file
+<DT><A HREF="jaligner/ui/filechooser/FileChooserJNLP.html#save(java.io.InputStream, java.lang.String)"><B>save(InputStream, String)</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A>
+<DD>Saves an input stream to a file.
+<DT><A HREF="jaligner/ui/filechooser/FileChooserTrusted.html#save(java.io.InputStream, java.lang.String)"><B>save(InputStream, String)</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A>
+<DD>Saves an input stream to a file.
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#save(javax.swing.text.JTextComponent, java.lang.String)"><B>save(JTextComponent, String)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Saves the contents of a text component to a file.
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#save(javax.swing.text.JTextComponent)"><B>save(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Saves the contents of a text component to a file.
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#selectAll(javax.swing.text.JTextComponent)"><B>selectAll(JTextComponent)</B></A> -
+Static method in class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>Selects all contents of a text component.
+<DT><A HREF="jaligner/Cell.html#set(int, int, float)"><B>set(int, int, float)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>Sets the row, column and score of the cell.
+<DT><A HREF="jaligner/Cell.html#setCol(int)"><B>setCol(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandler.html#setContents(java.lang.String)"><B>setContents(String)</B></A> -
+Method in interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A>
+<DD>Sets the contents of the system of the clipboard
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html#setContents(java.lang.String)"><B>setContents(String)</B></A> -
+Method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A>
+<DD>Sets the contents of the system clipboard
+<DT><A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html#setContents(java.lang.String)"><B>setContents(String)</B></A> -
+Method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A>
+<DD>Sets the contents of the system clipboard
+<DT><A HREF="jaligner/Sequence.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Sets the sequence description
+<DT><A HREF="jaligner/Alignment.html#setExtend(float)"><B>setExtend(float)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setGaps(int)"><B>setGaps(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Sequence.html#setId(java.lang.String)"><B>setId(String)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Sets the sequence id
+<DT><A HREF="jaligner/formats/Format.html#setId(java.lang.String)"><B>setId(String)</B></A> -
+Method in class jaligner.formats.<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats">Format</A>
+<DD>Sets format id
+<DT><A HREF="jaligner/Alignment.html#setIdentity(int)"><B>setIdentity(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/util/Commons.html#setJnlp(boolean)"><B>setJnlp(boolean)</B></A> -
+Static method in class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util">Commons</A>
+<DD>Sets the JNLP flag to true of false
+<DT><A HREF="jaligner/Alignment.html#setMarkupLine(char[])"><B>setMarkupLine(char[])</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setMatrix(jaligner.matrix.Matrix)"><B>setMatrix(Matrix)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setName1(java.lang.String)"><B>setName1(String)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setName2(java.lang.String)"><B>setName2(String)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setOpen(float)"><B>setOpen(float)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Cell.html#setRow(int)"><B>setRow(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setScore(float)"><B>setScore(float)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Cell.html#setScore(float)"><B>setScore(float)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner">Cell</A>
+<DD>
+<DT><A HREF="jaligner/Sequence.html#setSequence(java.lang.String)"><B>setSequence(String)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Sets the sequence string
+<DT><A HREF="jaligner/Alignment.html#setSequence1(char[])"><B>setSequence1(char[])</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setSequence2(char[])"><B>setSequence2(char[])</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setSimilarity(int)"><B>setSimilarity(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setStart1(int)"><B>setStart1(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Alignment.html#setStart2(int)"><B>setStart2(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner">Alignment</A>
+<DD>
+<DT><A HREF="jaligner/Sequence.html#setType(int)"><B>setType(int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Sets the sequence type (nucleic or protein)
+<DT><A HREF="jaligner/ui/filechooser/FileChooser.html#setUserDirectory(java.lang.String)"><B>setUserDirectory(String)</B></A> -
+Method in class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A>
+<DD>Sets the user working directory
+<DT><A HREF="jaligner/ui/clipboard/ClipboardPoller.html#start()"><B>start()</B></A> -
+Method in class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard">ClipboardPoller</A>
+<DD>Starts the thread
+<DT><A HREF="jaligner/Sequence.html#subsequence(int, int)"><B>subsequence(int, int)</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns a subsequence
+</DL>
+<HR>
+<A NAME="_T_"><!-- --></A><H2>
+<B>T</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><B>TextComponentUtil</B></A> - class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>.<DD>Text component (e.g.<DT><A HREF="jaligner/ui/util/TextComponentUtil.html#TextComponentUtil()"><B>TextComponentUtil()</B></A> -
+Constructor for class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A>
+<DD>
+<DT><A HREF="jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util"><B>TextComponentUtilException</B></A> - exception jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A>.<DD> <DT><A HREF="jaligner/ui/util/TextComponentUtilException.html#TextComponentUtilException(java.lang.String)"><B>TextComponentUtilException(String)</B></A> -
+Constructor for class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A>
+<DD>
+<DT><A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images"><B>ToolbarIcons</B></A> - class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>.<DD>Toolbar icons<DT><A HREF="jaligner/ui/images/ToolbarIcons.html#ToolbarIcons()"><B>ToolbarIcons()</B></A> -
+Constructor for class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A>
+<DD>
+<DT><A HREF="jaligner/Sequence.html#toArray()"><B>toArray()</B></A> -
+Method in class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner">Sequence</A>
+<DD>Returns the sequence as an array of characters.
+</DL>
+<HR>
+<A NAME="_U_"><!-- --></A><H2>
+<B>U</B></H2>
+<DL>
+<DT><A HREF="jaligner/Directions.html#UP"><B>UP</B></A> -
+Static variable in class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner">Directions</A>
+<DD>Traceback direction up
+</DL>
+<HR>
+<A NAME="_W_"><!-- --></A><H2>
+<B>W</B></H2>
+<DL>
+<DT><A HREF="jaligner/ui/util/PrintJobMointor.html#waitForPrintJob()"><B>waitForPrintJob()</B></A> -
+Method in class jaligner.ui.util.<A HREF="jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util">PrintJobMointor</A>
+<DD>Waits for print job
+</DL>
+<HR>
+<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_I_">I</A> <A HREF="#_J_">J</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_W_">W</A>
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="index-all.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/index.html b/api/index.html
new file mode 100644
index 0000000..9491146
--- /dev/null
+++ b/api/index.html
@@ -0,0 +1,26 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Frameset//EN" "http://www.w3.org/TR/html4/frameset.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Tue May 03 15:20:23 PDT 2005-->
+<TITLE>
+JAligner
+</TITLE>
+</HEAD>
+<FRAMESET cols="20%,80%">
+<FRAMESET rows="30%,70%">
+<FRAME src="overview-frame.html" name="packageListFrame" title="All Packages">
+<FRAME src="allclasses-frame.html" name="packageFrame" title="All classes and interfaces (except non-static nested types)">
+</FRAMESET>
+<FRAME src="overview-summary.html" name="classFrame" title="Package, class and interface descriptions">
+<NOFRAMES>
+<H2>
+Frame Alert</H2>
+
+<P>
+This document is designed to be viewed using the frames feature. If you see this message, you are using a non-frame-capable web client.
+<BR>
+Link to<A HREF="overview-summary.html">Non-frame version.</A>
+</NOFRAMES>
+</FRAMESET>
+</HTML>
diff --git a/api/jaligner.css b/api/jaligner.css
new file mode 100644
index 0000000..6ec4b14
--- /dev/null
+++ b/api/jaligner.css
@@ -0,0 +1,38 @@
+/* ahmed.css -- default style sheet */
+
+BODY {
+color: black;
+background: white;
+font-family: Arial, Times, Courier, serif;
+margin-left: 2.5%;
+margin-right: 2.5%;
+<!-- font-size: 85%; -->
+}
+
+A:link {
+color: navy;
+text-decoration: none;
+}
+
+A:visited {
+color: purple;
+text-decoration: none;
+}
+
+A:hover {
+background: yellow;
+text-decoration: none;
+}
+
+A:active {
+background: cyan;
+text-decoration: none;
+}
+
+P, BLOCKQUOTE {
+text-align:justify;
+}
+
+UL {
+/*text-align:left;*/
+}
diff --git a/api/jaligner/Alignment.html b/api/jaligner/Alignment.html
new file mode 100644
index 0000000..2c86f4f
--- /dev/null
+++ b/api/jaligner/Alignment.html
@@ -0,0 +1,891 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Alignment (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.Alignment class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Alignment (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Alignment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../jaligner/Cell.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner</FONT>
+<BR>
+Class Alignment</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../resources/inherit.gif" ALT="extended by"><B>jaligner.Alignment</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Alignment</B><DT>extends java.lang.Object</DL>
+
+<P>
+Holds the output of a pairwise sequences alignment.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#GAP">GAP</A></B></CODE>
+
+<BR>
+ Gap character</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#Alignment()">Alignment</A></B>()</CODE>
+
+<BR>
+ Constructor for Alignment</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#calculateScore()">calculateScore</A></B>()</CODE>
+
+<BR>
+ Calculate the score of the alignment, not using the score field (the
+ function only uses sequence1, sequence2, matrix and gap penalties).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#checkScore()">checkScore</A></B>()</CODE>
+
+<BR>
+ Check if the calculated score matches the field score.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getExtend()">getExtend</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getGaps()">getGaps</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getIdentity()">getIdentity</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getMarkupLine()">getMarkupLine</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getMatrix()">getMatrix</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getName1()">getName1</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getName2()">getName2</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getOpen()">getOpen</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getScore()">getScore</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getSequence1()">getSequence1</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getSequence2()">getSequence2</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getSimilarity()">getSimilarity</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getStart1()">getStart1</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getStart2()">getStart2</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#getSummary()">getSummary</A></B>()</CODE>
+
+<BR>
+ Returns a summary for alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setExtend(float)">setExtend</A></B>(float extend)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setGaps(int)">setGaps</A></B>(int gaps)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setIdentity(int)">setIdentity</A></B>(int identity)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setMarkupLine(char[])">setMarkupLine</A></B>(char[] markupLine)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setMatrix(jaligner.matrix.Matrix)">setMatrix</A></B>(<A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setName1(java.lang.String)">setName1</A></B>(java.lang.String name1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setName2(java.lang.String)">setName2</A></B>(java.lang.String name2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setOpen(float)">setOpen</A></B>(float open)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setScore(float)">setScore</A></B>(float score)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setSequence1(char[])">setSequence1</A></B>(char[] sequence1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setSequence2(char[])">setSequence2</A></B>(char[] sequence2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setSimilarity(int)">setSimilarity</A></B>(int similarity)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setStart1(int)">setStart1</A></B>(int start1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Alignment.html#setStart2(int)">setStart2</A></B>(int start2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GAP"><!-- --></A><H3>
+GAP</H3>
+<PRE>
+public static final char <B>GAP</B></PRE>
+<DL>
+<DD>Gap character
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Alignment.GAP">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Alignment()"><!-- --></A><H3>
+Alignment</H3>
+<PRE>
+public <B>Alignment</B>()</PRE>
+<DL>
+<DD>Constructor for Alignment
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getExtend()"><!-- --></A><H3>
+getExtend</H3>
+<PRE>
+public float <B>getExtend</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the extend.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setExtend(float)"><!-- --></A><H3>
+setExtend</H3>
+<PRE>
+public void <B>setExtend</B>(float extend)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>extend</CODE> - The extend to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMatrix()"><!-- --></A><H3>
+getMatrix</H3>
+<PRE>
+public <A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> <B>getMatrix</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the matrix.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMatrix(jaligner.matrix.Matrix)"><!-- --></A><H3>
+setMatrix</H3>
+<PRE>
+public void <B>setMatrix</B>(<A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>matrix</CODE> - The matrix to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName1()"><!-- --></A><H3>
+getName1</H3>
+<PRE>
+public java.lang.String <B>getName1</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the name1.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setName1(java.lang.String)"><!-- --></A><H3>
+setName1</H3>
+<PRE>
+public void <B>setName1</B>(java.lang.String name1)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>name1</CODE> - The name1 to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName2()"><!-- --></A><H3>
+getName2</H3>
+<PRE>
+public java.lang.String <B>getName2</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the name2.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setName2(java.lang.String)"><!-- --></A><H3>
+setName2</H3>
+<PRE>
+public void <B>setName2</B>(java.lang.String name2)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>name2</CODE> - The name2 to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOpen()"><!-- --></A><H3>
+getOpen</H3>
+<PRE>
+public float <B>getOpen</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the open.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOpen(float)"><!-- --></A><H3>
+setOpen</H3>
+<PRE>
+public void <B>setOpen</B>(float open)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>open</CODE> - The open to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScore()"><!-- --></A><H3>
+getScore</H3>
+<PRE>
+public float <B>getScore</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the score.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setScore(float)"><!-- --></A><H3>
+setScore</H3>
+<PRE>
+public void <B>setScore</B>(float score)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>score</CODE> - The score to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequence1()"><!-- --></A><H3>
+getSequence1</H3>
+<PRE>
+public char[] <B>getSequence1</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the sequence1.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequence1(char[])"><!-- --></A><H3>
+setSequence1</H3>
+<PRE>
+public void <B>setSequence1</B>(char[] sequence1)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence1</CODE> - The sequence1 to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequence2()"><!-- --></A><H3>
+getSequence2</H3>
+<PRE>
+public char[] <B>getSequence2</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the sequence2.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequence2(char[])"><!-- --></A><H3>
+setSequence2</H3>
+<PRE>
+public void <B>setSequence2</B>(char[] sequence2)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence2</CODE> - The sequence2 to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getStart1()"><!-- --></A><H3>
+getStart1</H3>
+<PRE>
+public int <B>getStart1</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the start1.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setStart1(int)"><!-- --></A><H3>
+setStart1</H3>
+<PRE>
+public void <B>setStart1</B>(int start1)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>start1</CODE> - The start1 to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getStart2()"><!-- --></A><H3>
+getStart2</H3>
+<PRE>
+public int <B>getStart2</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the start2.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setStart2(int)"><!-- --></A><H3>
+setStart2</H3>
+<PRE>
+public void <B>setStart2</B>(int start2)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>start2</CODE> - The start2 to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGaps()"><!-- --></A><H3>
+getGaps</H3>
+<PRE>
+public int <B>getGaps</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the gaps.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setGaps(int)"><!-- --></A><H3>
+setGaps</H3>
+<PRE>
+public void <B>setGaps</B>(int gaps)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>gaps</CODE> - The gaps to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentity()"><!-- --></A><H3>
+getIdentity</H3>
+<PRE>
+public int <B>getIdentity</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the identity.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setIdentity(int)"><!-- --></A><H3>
+setIdentity</H3>
+<PRE>
+public void <B>setIdentity</B>(int identity)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identity</CODE> - The identity to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMarkupLine()"><!-- --></A><H3>
+getMarkupLine</H3>
+<PRE>
+public char[] <B>getMarkupLine</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the markupLine.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMarkupLine(char[])"><!-- --></A><H3>
+setMarkupLine</H3>
+<PRE>
+public void <B>setMarkupLine</B>(char[] markupLine)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>markupLine</CODE> - The markupLine to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSimilarity()"><!-- --></A><H3>
+getSimilarity</H3>
+<PRE>
+public int <B>getSimilarity</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the similarity.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSimilarity(int)"><!-- --></A><H3>
+setSimilarity</H3>
+<PRE>
+public void <B>setSimilarity</B>(int similarity)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>similarity</CODE> - The similarity to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSummary()"><!-- --></A><H3>
+getSummary</H3>
+<PRE>
+public java.lang.String <B>getSummary</B>()</PRE>
+<DL>
+<DD>Returns a summary for alignment
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>alignment summary</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calculateScore()"><!-- --></A><H3>
+calculateScore</H3>
+<PRE>
+public float <B>calculateScore</B>()</PRE>
+<DL>
+<DD>Calculate the score of the alignment, not using the score field (the
+ function only uses sequence1, sequence2, matrix and gap penalties). (By:
+ Bram Minnaert)
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the calculated score</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkScore()"><!-- --></A><H3>
+checkScore</H3>
+<PRE>
+public boolean <B>checkScore</B>()</PRE>
+<DL>
+<DD>Check if the calculated score matches the field score.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>true if equal, else false. (By: Bram Minnaert)</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Alignment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../jaligner/Cell.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/Cell.html b/api/jaligner/Cell.html
new file mode 100644
index 0000000..6322e35
--- /dev/null
+++ b/api/jaligner/Cell.html
@@ -0,0 +1,385 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Cell (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.Cell class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Cell (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Cell.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Alignment.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/Directions.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Cell.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner</FONT>
+<BR>
+Class Cell</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../resources/inherit.gif" ALT="extended by"><B>jaligner.Cell</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Cell</B><DT>extends java.lang.Object</DL>
+
+<P>
+A cell in a similarity matrix, to hold row, column and score.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Cell.html#Cell()">Cell</A></B>()</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#getCol()">getCol</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#getRow()">getRow</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#getScore()">getScore</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#set(int, int, float)">set</A></B>(int row,
+ int col,
+ float score)</CODE>
+
+<BR>
+ Sets the row, column and score of the cell.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#setCol(int)">setCol</A></B>(int col)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#setRow(int)">setRow</A></B>(int row)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Cell.html#setScore(float)">setScore</A></B>(float score)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Cell()"><!-- --></A><H3>
+Cell</H3>
+<PRE>
+public <B>Cell</B>()</PRE>
+<DL>
+<DD>Constructor
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getCol()"><!-- --></A><H3>
+getCol</H3>
+<PRE>
+public int <B>getCol</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the col.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setCol(int)"><!-- --></A><H3>
+setCol</H3>
+<PRE>
+public void <B>setCol</B>(int col)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>col</CODE> - The col to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRow()"><!-- --></A><H3>
+getRow</H3>
+<PRE>
+public int <B>getRow</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the row.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setRow(int)"><!-- --></A><H3>
+setRow</H3>
+<PRE>
+public void <B>setRow</B>(int row)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>row</CODE> - The row to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScore()"><!-- --></A><H3>
+getScore</H3>
+<PRE>
+public float <B>getScore</B>()</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the score.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setScore(float)"><!-- --></A><H3>
+setScore</H3>
+<PRE>
+public void <B>setScore</B>(float score)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>score</CODE> - The score to set.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="set(int, int, float)"><!-- --></A><H3>
+set</H3>
+<PRE>
+public void <B>set</B>(int row,
+ int col,
+ float score)</PRE>
+<DL>
+<DD>Sets the row, column and score of the cell.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>row</CODE> - The row to set.<DD><CODE>col</CODE> - The col to set.<DD><CODE>score</CODE> - The score to set.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Cell.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Alignment.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/Directions.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Cell.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/Directions.html b/api/jaligner/Directions.html
new file mode 100644
index 0000000..bc7e865
--- /dev/null
+++ b/api/jaligner/Directions.html
@@ -0,0 +1,321 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Directions (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.Directions class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Directions (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Directions.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Cell.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/Markups.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Directions.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner</FONT>
+<BR>
+Class Directions</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../resources/inherit.gif" ALT="extended by"><B>jaligner.Directions</B>
+</PRE>
+<HR>
+<DL>
+<DT>public abstract class <B>Directions</B><DT>extends java.lang.Object</DL>
+
+<P>
+Traceback directions.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static byte</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Directions.html#DIAGONAL">DIAGONAL</A></B></CODE>
+
+<BR>
+ Traceback direction diagonal</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static byte</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Directions.html#LEFT">LEFT</A></B></CODE>
+
+<BR>
+ Traceback direction left</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static byte</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Directions.html#STOP">STOP</A></B></CODE>
+
+<BR>
+ Traceback direction stop</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static byte</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Directions.html#UP">UP</A></B></CODE>
+
+<BR>
+ Traceback direction up</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Directions.html#Directions()">Directions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="STOP"><!-- --></A><H3>
+STOP</H3>
+<PRE>
+public static final byte <B>STOP</B></PRE>
+<DL>
+<DD>Traceback direction stop
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Directions.STOP">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="LEFT"><!-- --></A><H3>
+LEFT</H3>
+<PRE>
+public static final byte <B>LEFT</B></PRE>
+<DL>
+<DD>Traceback direction left
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Directions.LEFT">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="DIAGONAL"><!-- --></A><H3>
+DIAGONAL</H3>
+<PRE>
+public static final byte <B>DIAGONAL</B></PRE>
+<DL>
+<DD>Traceback direction diagonal
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Directions.DIAGONAL">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="UP"><!-- --></A><H3>
+UP</H3>
+<PRE>
+public static final byte <B>UP</B></PRE>
+<DL>
+<DD>Traceback direction up
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Directions.UP">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Directions()"><!-- --></A><H3>
+Directions</H3>
+<PRE>
+public <B>Directions</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Directions.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Cell.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/Markups.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Directions.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/Markups.html b/api/jaligner/Markups.html
new file mode 100644
index 0000000..7fae6a8
--- /dev/null
+++ b/api/jaligner/Markups.html
@@ -0,0 +1,321 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Markups (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.Markups class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Markups (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Markups.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Directions.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/Sequence.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Markups.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner</FONT>
+<BR>
+Class Markups</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../resources/inherit.gif" ALT="extended by"><B>jaligner.Markups</B>
+</PRE>
+<HR>
+<DL>
+<DT>public abstract class <B>Markups</B><DT>extends java.lang.Object</DL>
+
+<P>
+Markups line characters.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Markups.html#GAP">GAP</A></B></CODE>
+
+<BR>
+ Markup line gap character</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Markups.html#IDENTITY">IDENTITY</A></B></CODE>
+
+<BR>
+ Markup line identity character</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Markups.html#MISMATCH">MISMATCH</A></B></CODE>
+
+<BR>
+ Markup line mismatch character</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Markups.html#SIMILARITY">SIMILARITY</A></B></CODE>
+
+<BR>
+ Markup line similarity character</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Markups.html#Markups()">Markups</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IDENTITY"><!-- --></A><H3>
+IDENTITY</H3>
+<PRE>
+public static final char <B>IDENTITY</B></PRE>
+<DL>
+<DD>Markup line identity character
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Markups.IDENTITY">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="SIMILARITY"><!-- --></A><H3>
+SIMILARITY</H3>
+<PRE>
+public static final char <B>SIMILARITY</B></PRE>
+<DL>
+<DD>Markup line similarity character
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Markups.SIMILARITY">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="GAP"><!-- --></A><H3>
+GAP</H3>
+<PRE>
+public static final char <B>GAP</B></PRE>
+<DL>
+<DD>Markup line gap character
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Markups.GAP">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="MISMATCH"><!-- --></A><H3>
+MISMATCH</H3>
+<PRE>
+public static final char <B>MISMATCH</B></PRE>
+<DL>
+<DD>Markup line mismatch character
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Markups.MISMATCH">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Markups()"><!-- --></A><H3>
+Markups</H3>
+<PRE>
+public <B>Markups</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Markups.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Directions.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/Sequence.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Markups.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/Sequence.html b/api/jaligner/Sequence.html
new file mode 100644
index 0000000..04b374a
--- /dev/null
+++ b/api/jaligner/Sequence.html
@@ -0,0 +1,635 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Sequence (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.Sequence class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Sequence (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Sequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Markups.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/SmithWatermanGotoh.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Sequence.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner</FONT>
+<BR>
+Class Sequence</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../resources/inherit.gif" ALT="extended by"><B>jaligner.Sequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>Sequence</B><DT>extends java.lang.Object<DT>implements java.io.Serializable</DL>
+
+<P>
+A basic (nucleic or protein) sequence. It's a wrapper to <CODE>String</CODE>.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../serialized-form.html#jaligner.Sequence">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#NUCLEIC">NUCLEIC</A></B></CODE>
+
+<BR>
+ Sequence type nucleic.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#PROTEIN">PROTEIN</A></B></CODE>
+
+<BR>
+ Sequence type protein.</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#Sequence()">Sequence</A></B>()</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#Sequence(java.lang.String)">Sequence</A></B>(java.lang.String sequence)</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#Sequence(java.lang.String, java.lang.String, java.lang.String, int)">Sequence</A></B>(java.lang.String sequence,
+ java.lang.String id,
+ java.lang.String description,
+ int type)</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#acidAt(int)">acidAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns the acid at specific location in the sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ Returns the sequence description</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#getId()">getId</A></B>()</CODE>
+
+<BR>
+ Returns the sequence id</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#getSequence()">getSequence</A></B>()</CODE>
+
+<BR>
+ Returns the sequence string</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#getType()">getType</A></B>()</CODE>
+
+<BR>
+ Returns the sequence type (nucleic or protein)</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#length()">length</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#setDescription(java.lang.String)">setDescription</A></B>(java.lang.String description)</CODE>
+
+<BR>
+ Sets the sequence description</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#setId(java.lang.String)">setId</A></B>(java.lang.String id)</CODE>
+
+<BR>
+ Sets the sequence id</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#setSequence(java.lang.String)">setSequence</A></B>(java.lang.String sequence)</CODE>
+
+<BR>
+ Sets the sequence string</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#setType(int)">setType</A></B>(int type)</CODE>
+
+<BR>
+ Sets the sequence type (nucleic or protein)</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#subsequence(int, int)">subsequence</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Returns a subsequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/Sequence.html#toArray()">toArray</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of characters.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NUCLEIC"><!-- --></A><H3>
+NUCLEIC</H3>
+<PRE>
+public static final int <B>NUCLEIC</B></PRE>
+<DL>
+<DD>Sequence type nucleic.
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Sequence.NUCLEIC">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="PROTEIN"><!-- --></A><H3>
+PROTEIN</H3>
+<PRE>
+public static final int <B>PROTEIN</B></PRE>
+<DL>
+<DD>Sequence type protein.
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../constant-values.html#jaligner.Sequence.PROTEIN">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Sequence()"><!-- --></A><H3>
+Sequence</H3>
+<PRE>
+public <B>Sequence</B>()</PRE>
+<DL>
+<DD>Constructor
+<P>
+</DL>
+<HR>
+
+<A NAME="Sequence(java.lang.String)"><!-- --></A><H3>
+Sequence</H3>
+<PRE>
+public <B>Sequence</B>(java.lang.String sequence)</PRE>
+<DL>
+<DD>Constructor
+<P>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - </DL>
+<HR>
+
+<A NAME="Sequence(java.lang.String, java.lang.String, java.lang.String, int)"><!-- --></A><H3>
+Sequence</H3>
+<PRE>
+public <B>Sequence</B>(java.lang.String sequence,
+ java.lang.String id,
+ java.lang.String description,
+ int type)</PRE>
+<DL>
+<DD>Constructor
+<P>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - <DD><CODE>id</CODE> - <DD><CODE>description</CODE> - <DD><CODE>type</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSequence()"><!-- --></A><H3>
+getSequence</H3>
+<PRE>
+public java.lang.String <B>getSequence</B>()</PRE>
+<DL>
+<DD>Returns the sequence string
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequence(java.lang.String)"><!-- --></A><H3>
+setSequence</H3>
+<PRE>
+public void <B>setSequence</B>(java.lang.String sequence)</PRE>
+<DL>
+<DD>Sets the sequence string
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - The sequence to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getId()"><!-- --></A><H3>
+getId</H3>
+<PRE>
+public java.lang.String <B>getId</B>()</PRE>
+<DL>
+<DD>Returns the sequence id
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the id</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setId(java.lang.String)"><!-- --></A><H3>
+setId</H3>
+<PRE>
+public void <B>setId</B>(java.lang.String id)</PRE>
+<DL>
+<DD>Sets the sequence id
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>id</CODE> - The id to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public java.lang.String <B>getDescription</B>()</PRE>
+<DL>
+<DD>Returns the sequence description
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the description</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>
+setDescription</H3>
+<PRE>
+public void <B>setDescription</B>(java.lang.String description)</PRE>
+<DL>
+<DD>Sets the sequence description
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>description</CODE> - The description to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getType()"><!-- --></A><H3>
+getType</H3>
+<PRE>
+public int <B>getType</B>()</PRE>
+<DL>
+<DD>Returns the sequence type (nucleic or protein)
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setType(int)"><!-- --></A><H3>
+setType</H3>
+<PRE>
+public void <B>setType</B>(int type)</PRE>
+<DL>
+<DD>Sets the sequence type (nucleic or protein)
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>type</CODE> - The type to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="length()"><!-- --></A><H3>
+length</H3>
+<PRE>
+public int <B>length</B>()</PRE>
+<DL>
+<DD>Returns the length of the sequence
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>sequence length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="subsequence(int, int)"><!-- --></A><H3>
+subsequence</H3>
+<PRE>
+public java.lang.String <B>subsequence</B>(int index,
+ int length)</PRE>
+<DL>
+<DD>Returns a subsequence
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - start index<DD><CODE>length</CODE> - length of subsequence
+<DT><B>Returns:</B><DD>subsequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="acidAt(int)"><!-- --></A><H3>
+acidAt</H3>
+<PRE>
+public char <B>acidAt</B>(int index)</PRE>
+<DL>
+<DD>Returns the acid at specific location in the sequence
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD>acid at index</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toArray()"><!-- --></A><H3>
+toArray</H3>
+<PRE>
+public char[] <B>toArray</B>()</PRE>
+<DL>
+<DD>Returns the sequence as an array of characters.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>array of chars.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Sequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Markups.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ <A HREF="../jaligner/SmithWatermanGotoh.html" title="class in jaligner"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Sequence.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/SmithWatermanGotoh.html b/api/jaligner/SmithWatermanGotoh.html
new file mode 100644
index 0000000..44dfd01
--- /dev/null
+++ b/api/jaligner/SmithWatermanGotoh.html
@@ -0,0 +1,247 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+SmithWatermanGotoh (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.SmithWatermanGotoh class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="SmithWatermanGotoh (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SmithWatermanGotoh.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Sequence.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SmithWatermanGotoh.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner</FONT>
+<BR>
+Class SmithWatermanGotoh</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../resources/inherit.gif" ALT="extended by"><B>jaligner.SmithWatermanGotoh</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SmithWatermanGotoh</B><DT>extends java.lang.Object</DL>
+
+<P>
+An implementation of the Smith-Waterman algorithm with Gotoh's improvement
+ for biological local pairwise sequence alignment.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../jaligner/Alignment.html" title="class in jaligner">Alignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../jaligner/SmithWatermanGotoh.html#align(jaligner.Sequence, jaligner.Sequence, jaligner.matrix.Matrix, float, float)">align</A></B>(<A HREF="../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s1,
+ <A HREF="../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s2,
+ <A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix,
+ float o,
+ float e)</CODE>
+
+<BR>
+ Aligns two sequences by Smith-Waterman algorithm</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="align(jaligner.Sequence, jaligner.Sequence, jaligner.matrix.Matrix, float, float)"><!-- --></A><H3>
+align</H3>
+<PRE>
+public static <A HREF="../jaligner/Alignment.html" title="class in jaligner">Alignment</A> <B>align</B>(<A HREF="../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s1,
+ <A HREF="../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s2,
+ <A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix,
+ float o,
+ float e)</PRE>
+<DL>
+<DD>Aligns two sequences by Smith-Waterman algorithm
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>s1</CODE> - sequene #1 (<A HREF="../jaligner/Sequence.html" title="class in jaligner"><CODE>Sequence</CODE></A>)<DD><CODE>s2</CODE> - sequene #2 (<A HREF="../jaligner/Sequence.html" title="class in jaligner"><CODE>Sequence</CODE></A>)<DD><CODE>matrix</CODE> - scoring matrix (<A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><CODE>Matrix</CODE></A>)<DD><CODE>o</CODE> - open gap penalty<DD><CODE>e</CODE> - extend gap penalty
+<DT><B>Returns:</B><DD>alignment object contains the two aligned sequences, the
+ alignment score and alignment statistics<DT><B>See Also:</B><DD><A HREF="../jaligner/Sequence.html" title="class in jaligner"><CODE>Sequence</CODE></A>,
+<A HREF="../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><CODE>Matrix</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SmithWatermanGotoh.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../jaligner/Sequence.html" title="class in jaligner"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SmithWatermanGotoh.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/class-use/Alignment.html b/api/jaligner/class-use/Alignment.html
new file mode 100644
index 0000000..a38c154
--- /dev/null
+++ b/api/jaligner/class-use/Alignment.html
@@ -0,0 +1,229 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.Alignment (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.Alignment (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Alignment.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.Alignment</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner"><B>jaligner</B></A></TD>
+<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.formats"><B>jaligner.formats</B></A></TD>
+<TD>Group of formats for output alignments. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> in <A HREF="../../jaligner/package-summary.html">jaligner</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../jaligner/package-summary.html">jaligner</A> that return <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A></CODE></FONT></TD>
+<TD><CODE><B>SmithWatermanGotoh.</B><B><A HREF="../../jaligner/SmithWatermanGotoh.html#align(jaligner.Sequence, jaligner.Sequence, jaligner.matrix.Matrix, float, float)">align</A></B>(<A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s1,
+ <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s2,
+ <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix,
+ float o,
+ float e)</CODE>
+
+<BR>
+ Aligns two sequences by Smith-Waterman algorithm</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.formats"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> in <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A> with parameters of type <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B>Pair.</B><B><A HREF="../../jaligner/formats/Pair.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Formats an alignment object to the Pair_FORMAT format</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract java.lang.String</CODE></FONT></TD>
+<TD><CODE><B>Format.</B><B><A HREF="../../jaligner/formats/Format.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Formats alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B>FASTA.</B><B><A HREF="../../jaligner/formats/FASTA.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B>CLUSTAL.</B><B><A HREF="../../jaligner/formats/CLUSTAL.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Returns CLUSTAL format of the alignment</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Alignment.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/class-use/Cell.html b/api/jaligner/class-use/Cell.html
new file mode 100644
index 0000000..8e63c82
--- /dev/null
+++ b/api/jaligner/class-use/Cell.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.Cell (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.Cell (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Cell.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Cell.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.Cell</B></H2>
+</CENTER>
+No usage of jaligner.Cell
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Cell.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Cell.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/class-use/Directions.html b/api/jaligner/class-use/Directions.html
new file mode 100644
index 0000000..f9fa532
--- /dev/null
+++ b/api/jaligner/class-use/Directions.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.Directions (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.Directions (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Directions.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Directions.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.Directions</B></H2>
+</CENTER>
+No usage of jaligner.Directions
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Directions.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Directions.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/class-use/Markups.html b/api/jaligner/class-use/Markups.html
new file mode 100644
index 0000000..f48ebb0
--- /dev/null
+++ b/api/jaligner/class-use/Markups.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.Markups (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.Markups (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Markups.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Markups.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.Markups</B></H2>
+</CENTER>
+No usage of jaligner.Markups
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Markups.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Markups.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/class-use/Sequence.html b/api/jaligner/class-use/Sequence.html
new file mode 100644
index 0000000..bbe3dee
--- /dev/null
+++ b/api/jaligner/class-use/Sequence.html
@@ -0,0 +1,242 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.Sequence (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.Sequence (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Sequence.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Sequence.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.Sequence</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner"><B>jaligner</B></A></TD>
+<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.formats"><B>jaligner.formats</B></A></TD>
+<TD>Group of formats for output alignments. </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.util"><B>jaligner.util</B></A></TD>
+<TD>Utility classes for helping core and GUI classes. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> in <A HREF="../../jaligner/package-summary.html">jaligner</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../jaligner/package-summary.html">jaligner</A> with parameters of type <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A></CODE></FONT></TD>
+<TD><CODE><B>SmithWatermanGotoh.</B><B><A HREF="../../jaligner/SmithWatermanGotoh.html#align(jaligner.Sequence, jaligner.Sequence, jaligner.matrix.Matrix, float, float)">align</A></B>(<A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s1,
+ <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s2,
+ <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix,
+ float o,
+ float e)</CODE>
+
+<BR>
+ Aligns two sequences by Smith-Waterman algorithm</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.formats"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> in <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A> with parameters of type <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B>FASTA.</B><B><A HREF="../../jaligner/formats/FASTA.html#format(jaligner.Sequence)">format</A></B>(<A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> sequence)</CODE>
+
+<BR>
+ Returns the name, description and sequence combined in one string.</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.util"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> in <A HREF="../../jaligner/util/package-summary.html">jaligner.util</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../jaligner/util/package-summary.html">jaligner.util</A> that return <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B>SequenceParser.</B><B><A HREF="../../jaligner/util/SequenceParser.html#parse(java.lang.String)">parse</A></B>(java.lang.String sequence)</CODE>
+
+<BR>
+ Returns a parsed Sequence from a string.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B>SequenceParser.</B><B><A HREF="../../jaligner/util/SequenceParser.html#parse(java.io.File)">parse</A></B>(java.io.File file)</CODE>
+
+<BR>
+ Returns a Sequence parsed and loaded from a file</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/Sequence.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Sequence.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/class-use/SmithWatermanGotoh.html b/api/jaligner/class-use/SmithWatermanGotoh.html
new file mode 100644
index 0000000..bd8d4e2
--- /dev/null
+++ b/api/jaligner/class-use/SmithWatermanGotoh.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.SmithWatermanGotoh (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.SmithWatermanGotoh (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/SmithWatermanGotoh.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SmithWatermanGotoh.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.SmithWatermanGotoh</B></H2>
+</CENTER>
+No usage of jaligner.SmithWatermanGotoh
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../jaligner/SmithWatermanGotoh.html" title="class in jaligner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SmithWatermanGotoh.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/example/Example.html b/api/jaligner/example/Example.html
new file mode 100644
index 0000000..2634eea
--- /dev/null
+++ b/api/jaligner/example/Example.html
@@ -0,0 +1,307 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Example (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.example.Example class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Example (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Example.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Example.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.example</FONT>
+<BR>
+Class Example</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.example.Example</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Example</B><DT>extends java.lang.Object</DL>
+
+<P>
+Example of using JAligner API to align P53 human aganist
+ P53 mouse using Smith-Waterman-Gotoh algorithm.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/example/Example.html#Example()">Example</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/example/Example.html#loadP53Human()">loadP53Human</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/example/Example.html#loadP53Mouse()">loadP53Mouse</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/example/Example.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Example()"><!-- --></A><H3>
+Example</H3>
+<PRE>
+public <B>Example</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(java.lang.String[] args)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="loadP53Human()"><!-- --></A><H3>
+loadP53Human</H3>
+<PRE>
+public static java.lang.String <B>loadP53Human</B>()
+ throws java.io.IOException</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>sequence string
+<DT><B>Throws:</B>
+<DD><CODE>java.io.IOException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="loadP53Mouse()"><!-- --></A><H3>
+loadP53Mouse</H3>
+<PRE>
+public static java.lang.String <B>loadP53Mouse</B>()
+ throws java.io.IOException</PRE>
+<DL>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>sequence string
+<DT><B>Throws:</B>
+<DD><CODE>java.io.IOException</CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Example.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Example.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/example/class-use/Example.html b/api/jaligner/example/class-use/Example.html
new file mode 100644
index 0000000..b9c936b
--- /dev/null
+++ b/api/jaligner/example/class-use/Example.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.example.Example (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.example.Example (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/example/Example.html" title="class in jaligner.example"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Example.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.example.Example</B></H2>
+</CENTER>
+No usage of jaligner.example.Example
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/example/Example.html" title="class in jaligner.example"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Example.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/example/package-frame.html b/api/jaligner/example/package-frame.html
new file mode 100644
index 0000000..1ab45f8
--- /dev/null
+++ b/api/jaligner/example/package-frame.html
@@ -0,0 +1,32 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner.example (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.example package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../jaligner/example/package-summary.html" target="classFrame">jaligner.example</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Example.html" title="class in jaligner.example" target="classFrame">Example</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/example/package-summary.html b/api/jaligner/example/package-summary.html
new file mode 100644
index 0000000..03c32a1
--- /dev/null
+++ b/api/jaligner/example/package-summary.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner.example (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.example package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.example (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/formats/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.example
+</H2>
+Example for using API of JAligner to perform pairwise sequence alignment.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/example/Example.html" title="class in jaligner.example">Example</A></B></TD>
+<TD>Example of using JAligner API to align P53 human aganist
+ P53 mouse using Smith-Waterman-Gotoh algorithm.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.example Description
+</H2>
+
+<P>
+Example for using API of JAligner to perform pairwise sequence alignment.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/formats/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/example/package-tree.html b/api/jaligner/example/package-tree.html
new file mode 100644
index 0000000..63c3ed5
--- /dev/null
+++ b/api/jaligner/example/package-tree.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner.example Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.example Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/formats/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.example
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.example.<A HREF="../../jaligner/example/Example.html" title="class in jaligner.example"><B>Example</B></A></UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/formats/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/example/package-use.html b/api/jaligner/example/package-use.html
new file mode 100644
index 0000000..8b8b603
--- /dev/null
+++ b/api/jaligner/example/package-use.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.example (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.example (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
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+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.example</B></H2>
+</CENTER>
+No usage of jaligner.example
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/CLUSTAL.html b/api/jaligner/formats/CLUSTAL.html
new file mode 100644
index 0000000..4c9b4a9
--- /dev/null
+++ b/api/jaligner/formats/CLUSTAL.html
@@ -0,0 +1,322 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+CLUSTAL (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats.CLUSTAL class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="CLUSTAL (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/CLUSTAL.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="CLUSTAL.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.formats</FONT>
+<BR>
+Class CLUSTAL</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">jaligner.formats.Format</A>
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.formats.CLUSTAL</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CLUSTAL</B><DT>extends <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></DL>
+
+<P>
+CLUSTAL format.
+ Example:
+ <pre>
+ <small>
+ CLUSTAL_FORMAT W(1.60) multiple sequence alignment
+
+
+ JC2395 NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
+ KPEL_DROME MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
+ FASA_MOUSE NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
+
+
+ JC2395 -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
+ KPEL_DROME -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
+ FASA_MOUSE -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
+
+
+ JC2395 IAEEIQAM
+ KPEL_DROME AMRLIKDY
+ FASA_MOUSE TLDKFQDM
+ </small>
+ </pre>
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/formats/CLUSTAL.html#CLUSTAL()">CLUSTAL</A></B>()</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/CLUSTAL.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Returns CLUSTAL format of the alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/CLUSTAL.html#format(java.lang.String[], java.lang.String[])">format</A></B>(java.lang.String[] names,
+ java.lang.String[] sequences)</CODE>
+
+<BR>
+ Returns CLUSTAL format</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_jaligner.formats.Format"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class jaligner.formats.<A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../jaligner/formats/Format.html#getId()">getId</A>, <A HREF="../../jaligner/formats/Format.html#setId(java.lang.String)">setId</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CLUSTAL()"><!-- --></A><H3>
+CLUSTAL</H3>
+<PRE>
+public <B>CLUSTAL</B>()</PRE>
+<DL>
+<DD>Constructor
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="format(java.lang.String[], java.lang.String[])"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(java.lang.String[] names,
+ java.lang.String[] sequences)</PRE>
+<DL>
+<DD>Returns CLUSTAL format
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>names</CODE> - array of the names of the sequences.<DD><CODE>sequences</CODE> - array of the sequences</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="format(jaligner.Alignment)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</PRE>
+<DL>
+<DD>Returns CLUSTAL format of the alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../jaligner/formats/Format.html#format(jaligner.Alignment)">format</A></CODE> in class <CODE><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> - (<A HREF="../../jaligner/Alignment.html" title="class in jaligner"><CODE>Alignment</CODE></A>)
+<DT><B>Returns:</B><DD>CLUSTAL format of the alignment<DT><B>See Also:</B><DD><A HREF="../../jaligner/Alignment.html" title="class in jaligner"><CODE>Alignment</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/CLUSTAL.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="CLUSTAL.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/FASTA.html b/api/jaligner/formats/FASTA.html
new file mode 100644
index 0000000..d0e94bb
--- /dev/null
+++ b/api/jaligner/formats/FASTA.html
@@ -0,0 +1,302 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FASTA (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats.FASTA class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FASTA (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FASTA.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FASTA.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.formats</FONT>
+<BR>
+Class FASTA</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">jaligner.formats.Format</A>
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.formats.FASTA</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>FASTA</B><DT>extends <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></DL>
+
+<P>
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/formats/FASTA.html#FASTA()">FASTA</A></B>()</CODE>
+
+<BR>
+ Constructor for FASTA.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/FASTA.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Formats alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/FASTA.html#format(jaligner.Sequence)">format</A></B>(<A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> sequence)</CODE>
+
+<BR>
+ Returns the name, description and sequence combined in one string.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_jaligner.formats.Format"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class jaligner.formats.<A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../jaligner/formats/Format.html#getId()">getId</A>, <A HREF="../../jaligner/formats/Format.html#setId(java.lang.String)">setId</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FASTA()"><!-- --></A><H3>
+FASTA</H3>
+<PRE>
+public <B>FASTA</B>()</PRE>
+<DL>
+<DD>Constructor for FASTA.
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="format(jaligner.Sequence)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(<A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> sequence)</PRE>
+<DL>
+<DD>Returns the name, description and sequence combined in one string.
+ The length of each line in the sequence is FASTA.LINE_LENGTH
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>String</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="format(jaligner.Alignment)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></CODE></B></DD>
+<DD>Formats alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../jaligner/formats/Format.html#format(jaligner.Alignment)">format</A></CODE> in class <CODE><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> -
+<DT><B>Returns:</B><DD>FASTA format of the input alignment<DT><B>See Also:</B><DD><A HREF="../../jaligner/Alignment.html" title="class in jaligner"><CODE>Alignment</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FASTA.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FASTA.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/Format.html b/api/jaligner/formats/Format.html
new file mode 100644
index 0000000..e2fa269
--- /dev/null
+++ b/api/jaligner/formats/Format.html
@@ -0,0 +1,309 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Format (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats.Format class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Format (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Format.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Format.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.formats</FONT>
+<BR>
+Class Format</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.formats.Format</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A>, <A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A>, <A HREF="../../jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>Format</B><DT>extends java.lang.Object</DL>
+
+<P>
+Abstract format
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/formats/Format.html#Format()">Format</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/Format.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Formats alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/Format.html#getId()">getId</A></B>()</CODE>
+
+<BR>
+ Returns format id</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/Format.html#setId(java.lang.String)">setId</A></B>(java.lang.String id)</CODE>
+
+<BR>
+ Sets format id</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Format()"><!-- --></A><H3>
+Format</H3>
+<PRE>
+public <B>Format</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="format(jaligner.Alignment)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public abstract java.lang.String <B>format</B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</PRE>
+<DL>
+<DD>Formats alignment
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> -
+<DT><B>Returns:</B><DD>formatted alignment<DT><B>See Also:</B><DD><A HREF="../../jaligner/Alignment.html" title="class in jaligner"><CODE>Alignment</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setId(java.lang.String)"><!-- --></A><H3>
+setId</H3>
+<PRE>
+public void <B>setId</B>(java.lang.String id)</PRE>
+<DL>
+<DD>Sets format id
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>id</CODE> - to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getId()"><!-- --></A><H3>
+getId</H3>
+<PRE>
+public java.lang.String <B>getId</B>()</PRE>
+<DL>
+<DD>Returns format id
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>id</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Format.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Format.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/FormatFactory.html b/api/jaligner/formats/FormatFactory.html
new file mode 100644
index 0000000..6c924a8
--- /dev/null
+++ b/api/jaligner/formats/FormatFactory.html
@@ -0,0 +1,301 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FormatFactory (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats.FormatFactory class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FormatFactory (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FormatFactory.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/formats/Pair.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FormatFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.formats</FONT>
+<BR>
+Class FormatFactory</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.formats.FormatFactory</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>FormatFactory</B><DT>extends java.lang.Object</DL>
+
+<P>
+Formats factory.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/FormatFactory.html#getFormat(java.lang.String)">getFormat</A></B>(java.lang.String id)</CODE>
+
+<BR>
+ Returns an instance of <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><CODE>Format</CODE></A>.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.util.Collection</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/FormatFactory.html#getFormats()">getFormats</A></B>()</CODE>
+
+<BR>
+ Returns a list of registered formats</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/FormatFactory.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ Returns an instance for <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><CODE>FormatFactory</CODE></A>.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/FormatFactory.html#registerFormat(jaligner.formats.Format)">registerFormat</A></B>(<A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A> format)</CODE>
+
+<BR>
+ Registers format.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD>Returns an instance for <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><CODE>FormatFactory</CODE></A>.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD><A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><CODE>FormatFactory</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="registerFormat(jaligner.formats.Format)"><!-- --></A><H3>
+registerFormat</H3>
+<PRE>
+public void <B>registerFormat</B>(<A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A> format)</PRE>
+<DL>
+<DD>Registers format.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>format</CODE> - instance of format</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFormat(java.lang.String)"><!-- --></A><H3>
+getFormat</H3>
+<PRE>
+public <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A> <B>getFormat</B>(java.lang.String id)</PRE>
+<DL>
+<DD>Returns an instance of <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><CODE>Format</CODE></A>.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>id</CODE> - format id
+<DT><B>Returns:</B><DD><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><CODE>Format</CODE></A> or null if id not found</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFormats()"><!-- --></A><H3>
+getFormats</H3>
+<PRE>
+public java.util.Collection <B>getFormats</B>()</PRE>
+<DL>
+<DD>Returns a list of registered formats
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD><CODE>Collection</CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FormatFactory.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/formats/Pair.html" title="class in jaligner.formats"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FormatFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/Pair.html b/api/jaligner/formats/Pair.html
new file mode 100644
index 0000000..082eafd
--- /dev/null
+++ b/api/jaligner/formats/Pair.html
@@ -0,0 +1,278 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Pair (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats.Pair class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Pair (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Pair.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Pair.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.formats</FONT>
+<BR>
+Class Pair</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">jaligner.formats.Format</A>
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.formats.Pair</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Pair</B><DT>extends <A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></DL>
+
+<P>
+<a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/formats/Pair.html#Pair()">Pair</A></B>()</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/formats/Pair.html#format(jaligner.Alignment)">format</A></B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</CODE>
+
+<BR>
+ Formats an alignment object to the Pair_FORMAT format</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_jaligner.formats.Format"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class jaligner.formats.<A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../jaligner/formats/Format.html#getId()">getId</A>, <A HREF="../../jaligner/formats/Format.html#setId(java.lang.String)">setId</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Pair()"><!-- --></A><H3>
+Pair</H3>
+<PRE>
+public <B>Pair</B>()</PRE>
+<DL>
+<DD>Constructor
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="format(jaligner.Alignment)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(<A HREF="../../jaligner/Alignment.html" title="class in jaligner">Alignment</A> alignment)</PRE>
+<DL>
+<DD>Formats an alignment object to the Pair_FORMAT format
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../jaligner/formats/Format.html#format(jaligner.Alignment)">format</A></CODE> in class <CODE><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> - alignment object to be formated
+<DT><B>Returns:</B><DD>string of the alignment pair-formatted<DT><B>See Also:</B><DD><A HREF="../../jaligner/Alignment.html" title="class in jaligner"><CODE>Alignment</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Pair.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Pair.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/class-use/CLUSTAL.html b/api/jaligner/formats/class-use/CLUSTAL.html
new file mode 100644
index 0000000..36b8354
--- /dev/null
+++ b/api/jaligner/formats/class-use/CLUSTAL.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.formats.CLUSTAL (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.formats.CLUSTAL (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="CLUSTAL.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.formats.CLUSTAL</B></H2>
+</CENTER>
+No usage of jaligner.formats.CLUSTAL
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="CLUSTAL.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/class-use/FASTA.html b/api/jaligner/formats/class-use/FASTA.html
new file mode 100644
index 0000000..04e0481
--- /dev/null
+++ b/api/jaligner/formats/class-use/FASTA.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.formats.FASTA (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.formats.FASTA (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FASTA.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.formats.FASTA</B></H2>
+</CENTER>
+No usage of jaligner.formats.FASTA
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FASTA.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/class-use/Format.html b/api/jaligner/formats/class-use/Format.html
new file mode 100644
index 0000000..63eec93
--- /dev/null
+++ b/api/jaligner/formats/class-use/Format.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.formats.Format (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.formats.Format (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Format.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.formats.Format</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.formats"><B>jaligner.formats</B></A></TD>
+<TD>Group of formats for output alignments. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.formats"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A> in <A HREF="../../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Subclasses of <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A> in <A HREF="../../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A></B></CODE>
+
+<BR>
+ CLUSTAL format.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A></B></CODE>
+
+<BR>
+ <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A></B></CODE>
+
+<BR>
+ <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/formats/package-summary.html">jaligner.formats</A> that return <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></CODE></FONT></TD>
+<TD><CODE><B>FormatFactory.</B><B><A HREF="../../../jaligner/formats/FormatFactory.html#getFormat(java.lang.String)">getFormat</A></B>(java.lang.String id)</CODE>
+
+<BR>
+ Returns an instance of <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats"><CODE>Format</CODE></A>.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/formats/package-summary.html">jaligner.formats</A> with parameters of type <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B>FormatFactory.</B><B><A HREF="../../../jaligner/formats/FormatFactory.html#registerFormat(jaligner.formats.Format)">registerFormat</A></B>(<A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A> format)</CODE>
+
+<BR>
+ Registers format.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/Format.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Format.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/class-use/FormatFactory.html b/api/jaligner/formats/class-use/FormatFactory.html
new file mode 100644
index 0000000..4b69f35
--- /dev/null
+++ b/api/jaligner/formats/class-use/FormatFactory.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.formats.FormatFactory (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.formats.FormatFactory (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FormatFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.formats.FormatFactory</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.formats"><B>jaligner.formats</B></A></TD>
+<TD>Group of formats for output alignments. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.formats"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A> in <A HREF="../../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/formats/package-summary.html">jaligner.formats</A> that return <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A></CODE></FONT></TD>
+<TD><CODE><B>FormatFactory.</B><B><A HREF="../../../jaligner/formats/FormatFactory.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ Returns an instance for <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><CODE>FormatFactory</CODE></A>.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FormatFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/class-use/Pair.html b/api/jaligner/formats/class-use/Pair.html
new file mode 100644
index 0000000..8c57367
--- /dev/null
+++ b/api/jaligner/formats/class-use/Pair.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.formats.Pair (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.formats.Pair (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/Pair.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Pair.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.formats.Pair</B></H2>
+</CENTER>
+No usage of jaligner.formats.Pair
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/formats/Pair.html" title="class in jaligner.formats"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Pair.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/package-frame.html b/api/jaligner/formats/package-frame.html
new file mode 100644
index 0000000..464aed5
--- /dev/null
+++ b/api/jaligner/formats/package-frame.html
@@ -0,0 +1,40 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner.formats (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../jaligner/formats/package-summary.html" target="classFrame">jaligner.formats</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CLUSTAL.html" title="class in jaligner.formats" target="classFrame">CLUSTAL</A>
+<BR>
+<A HREF="FASTA.html" title="class in jaligner.formats" target="classFrame">FASTA</A>
+<BR>
+<A HREF="Format.html" title="class in jaligner.formats" target="classFrame">Format</A>
+<BR>
+<A HREF="FormatFactory.html" title="class in jaligner.formats" target="classFrame">FormatFactory</A>
+<BR>
+<A HREF="Pair.html" title="class in jaligner.formats" target="classFrame">Pair</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/package-summary.html b/api/jaligner/formats/package-summary.html
new file mode 100644
index 0000000..d9ffa95
--- /dev/null
+++ b/api/jaligner/formats/package-summary.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner.formats (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.formats package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.formats (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/example/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/matrix/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.formats
+</H2>
+Group of formats for output alignments.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats">CLUSTAL</A></B></TD>
+<TD>CLUSTAL format.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats">FASTA</A></B></TD>
+<TD><a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats">Format</A></B></TD>
+<TD>Abstract format</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats">FormatFactory</A></B></TD>
+<TD>Formats factory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/formats/Pair.html" title="class in jaligner.formats">Pair</A></B></TD>
+<TD><a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.formats Description
+</H2>
+
+<P>
+Group of formats for output alignments.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/example/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/matrix/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/package-tree.html b/api/jaligner/formats/package-tree.html
new file mode 100644
index 0000000..7818733
--- /dev/null
+++ b/api/jaligner/formats/package-tree.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.formats Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.formats Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/example/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/matrix/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.formats
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.formats.<A HREF="../../jaligner/formats/Format.html" title="class in jaligner.formats"><B>Format</B></A><UL>
+<LI TYPE="circle">class jaligner.formats.<A HREF="../../jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><B>CLUSTAL</B></A><LI TYPE="circle">class jaligner.formats.<A HREF="../../jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>FASTA</B></A><LI TYPE="circle">class jaligner.formats.<A HREF="../../jaligner/formats/Pair.html" title="class in jaligner.formats"><B>Pair</B></A></UL>
+<LI TYPE="circle">class jaligner.formats.<A HREF="../../jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>FormatFactory</B></A></UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>
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+</TD>
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/example/package-tree.html"><B>PREV</B></A>
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+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/formats/package-use.html b/api/jaligner/formats/package-use.html
new file mode 100644
index 0000000..48485e9
--- /dev/null
+++ b/api/jaligner/formats/package-use.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.formats (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.formats (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
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+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
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+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
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+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.formats</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.formats"><B>jaligner.formats</B></A></TD>
+<TD>Group of formats for output alignments. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.formats"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A> used by <A HREF="../../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../jaligner/formats/class-use/Format.html#jaligner.formats"><B>Format</B></A></B>
+
+<BR>
+ Abstract format</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../jaligner/formats/class-use/FormatFactory.html#jaligner.formats"><B>FormatFactory</B></A></B>
+
+<BR>
+ Formats factory.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/MatricesCompartor.html b/api/jaligner/matrix/MatricesCompartor.html
new file mode 100644
index 0000000..41ec205
--- /dev/null
+++ b/api/jaligner/matrix/MatricesCompartor.html
@@ -0,0 +1,277 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+MatricesCompartor (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.matrix.MatricesCompartor class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="MatricesCompartor (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MatricesCompartor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatricesCompartor.html" target="_top"><B>NO FRAMES</B></A>
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+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.matrix</FONT>
+<BR>
+Class MatricesCompartor</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.matrix.MatricesCompartor</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.util.Comparator</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>MatricesCompartor</B><DT>extends java.lang.Object<DT>implements java.util.Comparator</DL>
+
+<P>
+Comparator to sort the scoring matrices by their names.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatricesCompartor.html#MatricesCompartor()">MatricesCompartor</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatricesCompartor.html#compare(java.lang.Object, java.lang.Object)">compare</A></B>(java.lang.Object o1,
+ java.lang.Object o2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.Comparator"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.util.Comparator</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>equals</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MatricesCompartor()"><!-- --></A><H3>
+MatricesCompartor</H3>
+<PRE>
+public <B>MatricesCompartor</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="compare(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+compare</H3>
+<PRE>
+public int <B>compare</B>(java.lang.Object o1,
+ java.lang.Object o2)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>compare</CODE> in interface <CODE>java.util.Comparator</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MatricesCompartor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatricesCompartor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/Matrix.html b/api/jaligner/matrix/Matrix.html
new file mode 100644
index 0000000..edcdfb4
--- /dev/null
+++ b/api/jaligner/matrix/Matrix.html
@@ -0,0 +1,317 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Matrix (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.matrix.Matrix class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Matrix (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Matrix.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Matrix.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.matrix</FONT>
+<BR>
+Class Matrix</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.matrix.Matrix</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>Matrix</B><DT>extends java.lang.Object<DT>implements java.io.Serializable</DL>
+
+<P>
+Scoring matrix.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#jaligner.matrix.Matrix">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/matrix/Matrix.html#Matrix(java.lang.String, float[][])">Matrix</A></B>(java.lang.String id,
+ float[][] scores)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/Matrix.html#getId()">getId</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/Matrix.html#getScore(char, char)">getScore</A></B>(char a,
+ char b)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> float[][]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/Matrix.html#getScores()">getScores</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Matrix(java.lang.String, float[][])"><!-- --></A><H3>
+Matrix</H3>
+<PRE>
+public <B>Matrix</B>(java.lang.String id,
+ float[][] scores)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getId()"><!-- --></A><H3>
+getId</H3>
+<PRE>
+public java.lang.String <B>getId</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the id.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScores()"><!-- --></A><H3>
+getScores</H3>
+<PRE>
+public float[][] <B>getScores</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the scores.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScore(char, char)"><!-- --></A><H3>
+getScore</H3>
+<PRE>
+public float <B>getScore</B>(char a,
+ char b)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>a</CODE> - <DD><CODE>b</CODE> -
+<DT><B>Returns:</B><DD>score</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Matrix.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><B>PREV CLASS</B></A>
+ <A HREF="../../jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Matrix.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/MatrixLoader.html b/api/jaligner/matrix/MatrixLoader.html
new file mode 100644
index 0000000..6994109
--- /dev/null
+++ b/api/jaligner/matrix/MatrixLoader.html
@@ -0,0 +1,342 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+MatrixLoader (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.matrix.MatrixLoader class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="MatrixLoader (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MatrixLoader.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoader.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.matrix</FONT>
+<BR>
+Class MatrixLoader</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.matrix.MatrixLoader</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>MatrixLoader</B><DT>extends java.lang.Object</DL>
+
+<P>
+Scoring matrices loader from a jar file or a file system.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatrixLoader.html#MatrixLoader()">MatrixLoader</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.util.Collection</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatrixLoader.html#list()">list</A></B>()</CODE>
+
+<BR>
+ Returns a list of the scoring matrices in the matrices home directory</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.util.Collection</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatrixLoader.html#list(boolean)">list</A></B>(boolean sort)</CODE>
+
+<BR>
+ Returns a list of the scoring matrices in the matrices home directory</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatrixLoader.html#load(jaligner.ui.filechooser.NamedInputStream)">load</A></B>(<A HREF="../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> nis)</CODE>
+
+<BR>
+ Loads scoring matrix from <CODE>InputStream</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatrixLoader.html#load(java.lang.String)">load</A></B>(java.lang.String matrix)</CODE>
+
+<BR>
+ Loads scoring matrix from Jar file or file system.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MatrixLoader()"><!-- --></A><H3>
+MatrixLoader</H3>
+<PRE>
+public <B>MatrixLoader</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load(java.lang.String)"><!-- --></A><H3>
+load</H3>
+<PRE>
+public static <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> <B>load</B>(java.lang.String matrix)
+ throws <A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></PRE>
+<DL>
+<DD>Loads scoring matrix from Jar file or file system.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>matrix</CODE> - to load
+<DT><B>Returns:</B><DD>loaded matrix
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><CODE>Matrix</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load(jaligner.ui.filechooser.NamedInputStream)"><!-- --></A><H3>
+load</H3>
+<PRE>
+public static <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> <B>load</B>(<A HREF="../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> nis)
+ throws <A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></PRE>
+<DL>
+<DD>Loads scoring matrix from <CODE>InputStream</CODE>
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>nis</CODE> - named input stream
+<DT><B>Returns:</B><DD>loaded matrix
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><CODE>Matrix</CODE></A>,
+<A HREF="../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><CODE>NamedInputStream</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="list(boolean)"><!-- --></A><H3>
+list</H3>
+<PRE>
+public static java.util.Collection <B>list</B>(boolean sort)
+ throws <A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></PRE>
+<DL>
+<DD>Returns a list of the scoring matrices in the matrices home directory
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sort</CODE> - flag to sort the list or not
+<DT><B>Returns:</B><DD>sorted array of scoring matrices
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="list()"><!-- --></A><H3>
+list</H3>
+<PRE>
+public static java.util.Collection <B>list</B>()
+ throws <A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></PRE>
+<DL>
+<DD>Returns a list of the scoring matrices in the matrices home directory
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>sorted array of scoring matrices
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MatrixLoader.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoader.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/MatrixLoaderException.html b/api/jaligner/matrix/MatrixLoaderException.html
new file mode 100644
index 0000000..5aab9dd
--- /dev/null
+++ b/api/jaligner/matrix/MatrixLoaderException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+MatrixLoaderException (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.matrix.MatrixLoaderException class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="MatrixLoaderException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MatrixLoaderException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoaderException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.matrix</FONT>
+<BR>
+Class MatrixLoaderException</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.lang.Throwable
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.lang.Exception
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.matrix.MatrixLoaderException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>MatrixLoaderException</B><DT>extends java.lang.Exception</DL>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#jaligner.matrix.MatrixLoaderException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/matrix/MatrixLoaderException.html#MatrixLoaderException(java.lang.String)">MatrixLoaderException</A></B>(java.lang.String message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Throwable</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MatrixLoaderException(java.lang.String)"><!-- --></A><H3>
+MatrixLoaderException</H3>
+<PRE>
+public <B>MatrixLoaderException</B>(java.lang.String message)</PRE>
+<DL>
+<DT><B>Parameters:</B><DD><CODE>message</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MatrixLoaderException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoaderException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/class-use/MatricesCompartor.html b/api/jaligner/matrix/class-use/MatricesCompartor.html
new file mode 100644
index 0000000..573acb8
--- /dev/null
+++ b/api/jaligner/matrix/class-use/MatricesCompartor.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.matrix.MatricesCompartor (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.matrix.MatricesCompartor (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatricesCompartor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.matrix.MatricesCompartor</B></H2>
+</CENTER>
+No usage of jaligner.matrix.MatricesCompartor
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <A HREF="MatricesCompartor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
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+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/class-use/Matrix.html b/api/jaligner/matrix/class-use/Matrix.html
new file mode 100644
index 0000000..4449af9
--- /dev/null
+++ b/api/jaligner/matrix/class-use/Matrix.html
@@ -0,0 +1,237 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.matrix.Matrix (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.matrix.Matrix (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Matrix.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.matrix.Matrix</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner"><B>jaligner</B></A></TD>
+<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.matrix"><B>jaligner.matrix</B></A></TD>
+<TD>Scoring matrices package. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> in <A HREF="../../../jaligner/package-summary.html">jaligner</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/package-summary.html">jaligner</A> that return <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B>Alignment.</B><B><A HREF="../../../jaligner/Alignment.html#getMatrix()">getMatrix</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/package-summary.html">jaligner</A> with parameters of type <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/Alignment.html" title="class in jaligner">Alignment</A></CODE></FONT></TD>
+<TD><CODE><B>SmithWatermanGotoh.</B><B><A HREF="../../../jaligner/SmithWatermanGotoh.html#align(jaligner.Sequence, jaligner.Sequence, jaligner.matrix.Matrix, float, float)">align</A></B>(<A HREF="../../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s1,
+ <A HREF="../../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> s2,
+ <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix,
+ float o,
+ float e)</CODE>
+
+<BR>
+ Aligns two sequences by Smith-Waterman algorithm</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B>Alignment.</B><B><A HREF="../../../jaligner/Alignment.html#setMatrix(jaligner.matrix.Matrix)">setMatrix</A></B>(<A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> matrix)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.matrix"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A> in <A HREF="../../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/matrix/package-summary.html">jaligner.matrix</A> that return <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../jaligner/matrix/MatrixLoader.html#load(java.lang.String)">load</A></B>(java.lang.String matrix)</CODE>
+
+<BR>
+ Loads scoring matrix from Jar file or file system.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../jaligner/matrix/MatrixLoader.html#load(jaligner.ui.filechooser.NamedInputStream)">load</A></B>(<A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> nis)</CODE>
+
+<BR>
+ Loads scoring matrix from <CODE>InputStream</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Matrix.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/class-use/MatrixLoader.html b/api/jaligner/matrix/class-use/MatrixLoader.html
new file mode 100644
index 0000000..9fb9197
--- /dev/null
+++ b/api/jaligner/matrix/class-use/MatrixLoader.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.matrix.MatrixLoader (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.matrix.MatrixLoader (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoader.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.matrix.MatrixLoader</B></H2>
+</CENTER>
+No usage of jaligner.matrix.MatrixLoader
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoader.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/class-use/MatrixLoaderException.html b/api/jaligner/matrix/class-use/MatrixLoaderException.html
new file mode 100644
index 0000000..11d1186
--- /dev/null
+++ b/api/jaligner/matrix/class-use/MatrixLoaderException.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.matrix.MatrixLoaderException (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.matrix.MatrixLoaderException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoaderException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.matrix.MatrixLoaderException</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.matrix"><B>jaligner.matrix</B></A></TD>
+<TD>Scoring matrices package. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.matrix"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A> in <A HREF="../../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/matrix/package-summary.html">jaligner.matrix</A> that throw <A HREF="../../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../jaligner/matrix/MatrixLoader.html#load(java.lang.String)">load</A></B>(java.lang.String matrix)</CODE>
+
+<BR>
+ Loads scoring matrix from Jar file or file system.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../jaligner/matrix/MatrixLoader.html#load(jaligner.ui.filechooser.NamedInputStream)">load</A></B>(<A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> nis)</CODE>
+
+<BR>
+ Loads scoring matrix from <CODE>InputStream</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.util.Collection</CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../jaligner/matrix/MatrixLoader.html#list(boolean)">list</A></B>(boolean sort)</CODE>
+
+<BR>
+ Returns a list of the scoring matrices in the matrices home directory</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.util.Collection</CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../jaligner/matrix/MatrixLoader.html#list()">list</A></B>()</CODE>
+
+<BR>
+ Returns a list of the scoring matrices in the matrices home directory</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="MatrixLoaderException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/package-frame.html b/api/jaligner/matrix/package-frame.html
new file mode 100644
index 0000000..fc579b3
--- /dev/null
+++ b/api/jaligner/matrix/package-frame.html
@@ -0,0 +1,47 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.matrix (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.matrix package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../jaligner/matrix/package-summary.html" target="classFrame">jaligner.matrix</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="MatricesCompartor.html" title="class in jaligner.matrix" target="classFrame">MatricesCompartor</A>
+<BR>
+<A HREF="Matrix.html" title="class in jaligner.matrix" target="classFrame">Matrix</A>
+<BR>
+<A HREF="MatrixLoader.html" title="class in jaligner.matrix" target="classFrame">MatrixLoader</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="MatrixLoaderException.html" title="class in jaligner.matrix" target="classFrame">MatrixLoaderException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/package-summary.html b/api/jaligner/matrix/package-summary.html
new file mode 100644
index 0000000..20e73a5
--- /dev/null
+++ b/api/jaligner/matrix/package-summary.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.matrix (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.matrix package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.matrix (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.matrix
+</H2>
+Scoring matrices package.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix">MatricesCompartor</A></B></TD>
+<TD>Comparator to sort the scoring matrices by their names.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></B></TD>
+<TD>Scoring matrix.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix">MatrixLoader</A></B></TD>
+<TD>Scoring matrices loader from a jar file or a file system.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">MatrixLoaderException</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.matrix Description
+</H2>
+
+<P>
+Scoring matrices package.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/package-tree.html b/api/jaligner/matrix/package-tree.html
new file mode 100644
index 0000000..bc71906
--- /dev/null
+++ b/api/jaligner/matrix/package-tree.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.matrix Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.matrix Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
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+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.matrix
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.matrix.<A HREF="../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><B>MatricesCompartor</B></A> (implements java.util.Comparator)
+<LI TYPE="circle">class jaligner.matrix.<A HREF="../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>Matrix</B></A> (implements java.io.Serializable)
+<LI TYPE="circle">class jaligner.matrix.<A HREF="../../jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><B>MatrixLoader</B></A><LI TYPE="circle">class java.lang.Throwable (implements java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.lang.Exception<UL>
+<LI TYPE="circle">class jaligner.matrix.<A HREF="../../jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix"><B>MatrixLoaderException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/formats/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/matrix/package-use.html b/api/jaligner/matrix/package-use.html
new file mode 100644
index 0000000..509ee6b
--- /dev/null
+++ b/api/jaligner/matrix/package-use.html
@@ -0,0 +1,187 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.matrix (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.matrix (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.matrix</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner"><B>jaligner</B></A></TD>
+<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.matrix"><B>jaligner.matrix</B></A></TD>
+<TD>Scoring matrices package. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../jaligner/matrix/package-summary.html">jaligner.matrix</A> used by <A HREF="../../jaligner/package-summary.html">jaligner</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../jaligner/matrix/class-use/Matrix.html#jaligner"><B>Matrix</B></A></B>
+
+<BR>
+ Scoring matrix.</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.matrix"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../jaligner/matrix/package-summary.html">jaligner.matrix</A> used by <A HREF="../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../jaligner/matrix/class-use/Matrix.html#jaligner.matrix"><B>Matrix</B></A></B>
+
+<BR>
+ Scoring matrix.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../jaligner/matrix/class-use/MatrixLoaderException.html#jaligner.matrix"><B>MatrixLoaderException</B></A></B>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/package-frame.html b/api/jaligner/package-frame.html
new file mode 100644
index 0000000..f02e5c4
--- /dev/null
+++ b/api/jaligner/package-frame.html
@@ -0,0 +1,42 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../jaligner/package-summary.html" target="classFrame">jaligner</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Alignment.html" title="class in jaligner" target="classFrame">Alignment</A>
+<BR>
+<A HREF="Cell.html" title="class in jaligner" target="classFrame">Cell</A>
+<BR>
+<A HREF="Directions.html" title="class in jaligner" target="classFrame">Directions</A>
+<BR>
+<A HREF="Markups.html" title="class in jaligner" target="classFrame">Markups</A>
+<BR>
+<A HREF="Sequence.html" title="class in jaligner" target="classFrame">Sequence</A>
+<BR>
+<A HREF="SmithWatermanGotoh.html" title="class in jaligner" target="classFrame">SmithWatermanGotoh</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/package-summary.html b/api/jaligner/package-summary.html
new file mode 100644
index 0000000..034b10a
--- /dev/null
+++ b/api/jaligner/package-summary.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV PACKAGE
+ <A HREF="../jaligner/example/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner
+</H2>
+Core classes for the implementation of Smith-Waterman-Gotoh algorithm
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../jaligner/Alignment.html" title="class in jaligner">Alignment</A></B></TD>
+<TD>Holds the output of a pairwise sequences alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../jaligner/Cell.html" title="class in jaligner">Cell</A></B></TD>
+<TD>A cell in a similarity matrix, to hold row, column and score.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../jaligner/Directions.html" title="class in jaligner">Directions</A></B></TD>
+<TD>Traceback directions.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../jaligner/Markups.html" title="class in jaligner">Markups</A></B></TD>
+<TD>Markups line characters.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../jaligner/Sequence.html" title="class in jaligner">Sequence</A></B></TD>
+<TD>A basic (nucleic or protein) sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../jaligner/SmithWatermanGotoh.html" title="class in jaligner">SmithWatermanGotoh</A></B></TD>
+<TD>An implementation of the Smith-Waterman algorithm with Gotoh's improvement
+ for biological local pairwise sequence alignment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner Description
+</H2>
+
+<P>
+Core classes for the implementation of Smith-Waterman-Gotoh algorithm
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV PACKAGE
+ <A HREF="../jaligner/example/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/package-tree.html b/api/jaligner/package-tree.html
new file mode 100644
index 0000000..6168855
--- /dev/null
+++ b/api/jaligner/package-tree.html
@@ -0,0 +1,146 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+jaligner Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ <A HREF="../jaligner/example/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.<A HREF="../jaligner/Alignment.html" title="class in jaligner"><B>Alignment</B></A><LI TYPE="circle">class jaligner.<A HREF="../jaligner/Cell.html" title="class in jaligner"><B>Cell</B></A><LI TYPE="circle">class jaligner.<A HREF="../jaligner/Directions.html" title="class in jaligner"><B>Directions</B></A><LI TYPE="circle">class jaligner.<A HREF="../jaligner/Markups.html" title="class in jaligner"><B>Markups</B></A><LI TYPE="circle">class jaligner.<A HREF [...]
+<LI TYPE="circle">class jaligner.<A HREF="../jaligner/SmithWatermanGotoh.html" title="class in jaligner"><B>SmithWatermanGotoh</B></A></UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ <A HREF="../jaligner/example/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/package-use.html b/api/jaligner/package-use.html
new file mode 100644
index 0000000..fc31388
--- /dev/null
+++ b/api/jaligner/package-use.html
@@ -0,0 +1,212 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../jaligner/package-summary.html">jaligner</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner"><B>jaligner</B></A></TD>
+<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.formats"><B>jaligner.formats</B></A></TD>
+<TD>Group of formats for output alignments. </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.util"><B>jaligner.util</B></A></TD>
+<TD>Utility classes for helping core and GUI classes. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../jaligner/package-summary.html">jaligner</A> used by <A HREF="../jaligner/package-summary.html">jaligner</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../jaligner/class-use/Alignment.html#jaligner"><B>Alignment</B></A></B>
+
+<BR>
+ Holds the output of a pairwise sequences alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../jaligner/class-use/Sequence.html#jaligner"><B>Sequence</B></A></B>
+
+<BR>
+ A basic (nucleic or protein) sequence.</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.formats"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../jaligner/package-summary.html">jaligner</A> used by <A HREF="../jaligner/formats/package-summary.html">jaligner.formats</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../jaligner/class-use/Alignment.html#jaligner.formats"><B>Alignment</B></A></B>
+
+<BR>
+ Holds the output of a pairwise sequences alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../jaligner/class-use/Sequence.html#jaligner.formats"><B>Sequence</B></A></B>
+
+<BR>
+ A basic (nucleic or protein) sequence.</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.util"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../jaligner/package-summary.html">jaligner</A> used by <A HREF="../jaligner/util/package-summary.html">jaligner.util</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../jaligner/class-use/Sequence.html#jaligner.util"><B>Sequence</B></A></B>
+
+<BR>
+ A basic (nucleic or protein) sequence.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/AlignmentScoreChecker.html b/api/jaligner/test/AlignmentScoreChecker.html
new file mode 100644
index 0000000..34d55db
--- /dev/null
+++ b/api/jaligner/test/AlignmentScoreChecker.html
@@ -0,0 +1,260 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+AlignmentScoreChecker (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.test.AlignmentScoreChecker class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="AlignmentScoreChecker (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignmentScoreChecker.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentScoreChecker.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.test</FONT>
+<BR>
+Class AlignmentScoreChecker</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.test.AlignmentScoreChecker</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignmentScoreChecker</B><DT>extends java.lang.Object</DL>
+
+<P>
+Testing the scores of the alignments of the SmithWaterman algorithm
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Bram Minnaert</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/test/AlignmentScoreChecker.html#AlignmentScoreChecker()">AlignmentScoreChecker</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/test/AlignmentScoreChecker.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentScoreChecker()"><!-- --></A><H3>
+AlignmentScoreChecker</H3>
+<PRE>
+public <B>AlignmentScoreChecker</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(java.lang.String[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignmentScoreChecker.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentScoreChecker.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/RandomSequenceGenerator.html b/api/jaligner/test/RandomSequenceGenerator.html
new file mode 100644
index 0000000..f487be4
--- /dev/null
+++ b/api/jaligner/test/RandomSequenceGenerator.html
@@ -0,0 +1,284 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+RandomSequenceGenerator (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.test.RandomSequenceGenerator class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="RandomSequenceGenerator (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RandomSequenceGenerator.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RandomSequenceGenerator.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.test</FONT>
+<BR>
+Class RandomSequenceGenerator</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.test.RandomSequenceGenerator</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>RandomSequenceGenerator</B><DT>extends java.lang.Object</DL>
+
+<P>
+This class contains a random generator for protein sequences.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Bram Minnaert</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/test/RandomSequenceGenerator.html#RandomSequenceGenerator()">RandomSequenceGenerator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/test/RandomSequenceGenerator.html#generate(int)">generate</A></B>(int length)</CODE>
+
+<BR>
+ Returns random sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/test/RandomSequenceGenerator.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
+
+<BR>
+ Displays 10 random protein sequences with length 50.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="RandomSequenceGenerator()"><!-- --></A><H3>
+RandomSequenceGenerator</H3>
+<PRE>
+public <B>RandomSequenceGenerator</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="generate(int)"><!-- --></A><H3>
+generate</H3>
+<PRE>
+public static java.lang.String <B>generate</B>(int length)</PRE>
+<DL>
+<DD>Returns random sequence
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>length</CODE> - Size of the sequence
+<DT><B>Returns:</B><DD>Random sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(java.lang.String[] args)</PRE>
+<DL>
+<DD>Displays 10 random protein sequences with length 50.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - no args</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RandomSequenceGenerator.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RandomSequenceGenerator.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/class-use/AlignmentScoreChecker.html b/api/jaligner/test/class-use/AlignmentScoreChecker.html
new file mode 100644
index 0000000..c047635
--- /dev/null
+++ b/api/jaligner/test/class-use/AlignmentScoreChecker.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.test.AlignmentScoreChecker (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.test.AlignmentScoreChecker (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentScoreChecker.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.test.AlignmentScoreChecker</B></H2>
+</CENTER>
+No usage of jaligner.test.AlignmentScoreChecker
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentScoreChecker.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/class-use/RandomSequenceGenerator.html b/api/jaligner/test/class-use/RandomSequenceGenerator.html
new file mode 100644
index 0000000..b623901
--- /dev/null
+++ b/api/jaligner/test/class-use/RandomSequenceGenerator.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.test.RandomSequenceGenerator (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.test.RandomSequenceGenerator (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RandomSequenceGenerator.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.test.RandomSequenceGenerator</B></H2>
+</CENTER>
+No usage of jaligner.test.RandomSequenceGenerator
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RandomSequenceGenerator.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/package-frame.html b/api/jaligner/test/package-frame.html
new file mode 100644
index 0000000..f364935
--- /dev/null
+++ b/api/jaligner/test/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.test (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.test package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../jaligner/test/package-summary.html" target="classFrame">jaligner.test</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentScoreChecker.html" title="class in jaligner.test" target="classFrame">AlignmentScoreChecker</A>
+<BR>
+<A HREF="RandomSequenceGenerator.html" title="class in jaligner.test" target="classFrame">RandomSequenceGenerator</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/package-summary.html b/api/jaligner/test/package-summary.html
new file mode 100644
index 0000000..6bb4b5e
--- /dev/null
+++ b/api/jaligner/test/package-summary.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.test (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.test package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.test (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/ui/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.test
+</H2>
+Testing package.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test">AlignmentScoreChecker</A></B></TD>
+<TD>Testing the scores of the alignments of the SmithWaterman algorithm</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test">RandomSequenceGenerator</A></B></TD>
+<TD>This class contains a random generator for protein sequences.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.test Description
+</H2>
+
+<P>
+Testing package.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Bram Minnaert</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/ui/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/package-tree.html b/api/jaligner/test/package-tree.html
new file mode 100644
index 0000000..2ea01ac
--- /dev/null
+++ b/api/jaligner/test/package-tree.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.test Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.test Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/ui/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.test
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.test.<A HREF="../../jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><B>AlignmentScoreChecker</B></A><LI TYPE="circle">class jaligner.test.<A HREF="../../jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><B>RandomSequenceGenerator</B></A></UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/matrix/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/ui/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/test/package-use.html b/api/jaligner/test/package-use.html
new file mode 100644
index 0000000..764a231
--- /dev/null
+++ b/api/jaligner/test/package-use.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.test (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.test (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.test</B></H2>
+</CENTER>
+No usage of jaligner.test
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/AlignCommandLine.html b/api/jaligner/ui/AlignCommandLine.html
new file mode 100644
index 0000000..4a4b2e0
--- /dev/null
+++ b/api/jaligner/ui/AlignCommandLine.html
@@ -0,0 +1,260 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+AlignCommandLine (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.AlignCommandLine class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="AlignCommandLine (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignCommandLine.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignCommandLine.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui</FONT>
+<BR>
+Class AlignCommandLine</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.AlignCommandLine</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignCommandLine</B><DT>extends java.lang.Object</DL>
+
+<P>
+Command line interface for JAligner.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignCommandLine.html#AlignCommandLine()">AlignCommandLine</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignCommandLine.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignCommandLine()"><!-- --></A><H3>
+AlignCommandLine</H3>
+<PRE>
+public <B>AlignCommandLine</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(java.lang.String[] args)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - The command line arguments</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignCommandLine.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignCommandLine.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/AlignWindow.html b/api/jaligner/ui/AlignWindow.html
new file mode 100644
index 0000000..9bfa4d2
--- /dev/null
+++ b/api/jaligner/ui/AlignWindow.html
@@ -0,0 +1,569 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+AlignWindow (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.AlignWindow class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="AlignWindow (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignWindow.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignWindow.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui</FONT>
+<BR>
+Class AlignWindow</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.awt.Component
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.awt.Container
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.awt.Window
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.awt.Frame
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">javax.swing.JFrame
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.AlignWindow</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>javax.accessibility.Accessible, <A HREF="../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A>, javax.swing.event.DocumentListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.io.Serializable, javax.swing.WindowConstants</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignWindow</B><DT>extends javax.swing.JFrame<DT>implements <A HREF="../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A>, javax.swing.event.DocumentListener</DL>
+
+<P>
+Graphical user inteface for JAligner.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#jaligner.ui.AlignWindow">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.JFrame</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>javax.swing.JFrame.AccessibleJFrame</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.Frame</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>java.awt.Frame.AccessibleAWTFrame</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.Window</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>java.awt.Window.AccessibleAWTWindow</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.Container</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>java.awt.Container.AccessibleAWTContainer</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.Component</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy</CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> javax.swing.Action</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#nextFocusAction">nextFocusAction</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> javax.swing.Action</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#prevFocusAction">prevFocusAction</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.JFrame</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.Frame</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.Component</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.WindowConstants</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.ImageObserver</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH</CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#AlignWindow()">AlignWindow</A></B>()</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#changedUpdate(javax.swing.event.DocumentEvent)">changedUpdate</A></B>(javax.swing.event.DocumentEvent e)</CODE>
+
+<BR>
+ Implements changedUpdate of <CODE>DocumentListener</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#clipboardCheck(java.lang.String)">clipboardCheck</A></B>(java.lang.String clipboardContents)</CODE>
+
+<BR>
+ Implements the notify method of the interface <A HREF="../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardListener</CODE></A></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#insertUpdate(javax.swing.event.DocumentEvent)">insertUpdate</A></B>(javax.swing.event.DocumentEvent e)</CODE>
+
+<BR>
+ Implements insertUpdate of <CODE>DocumentListener</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/ui/AlignWindow.html#removeUpdate(javax.swing.event.DocumentEvent)">removeUpdate</A></B>(javax.swing.event.DocumentEvent e)</CODE>
+
+<BR>
+ Implements removeUpdate of <CODE>DocumentListener</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.JFrame</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.Frame</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setIconImage, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.Window</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWind [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.Container</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicySet [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.Component</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePrope [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.MenuContainer</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>getFont, postEvent</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="nextFocusAction"><!-- --></A><H3>
+nextFocusAction</H3>
+<PRE>
+public javax.swing.Action <B>nextFocusAction</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="prevFocusAction"><!-- --></A><H3>
+prevFocusAction</H3>
+<PRE>
+public javax.swing.Action <B>prevFocusAction</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignWindow()"><!-- --></A><H3>
+AlignWindow</H3>
+<PRE>
+public <B>AlignWindow</B>()</PRE>
+<DL>
+<DD>Constructor
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="insertUpdate(javax.swing.event.DocumentEvent)"><!-- --></A><H3>
+insertUpdate</H3>
+<PRE>
+public void <B>insertUpdate</B>(javax.swing.event.DocumentEvent e)</PRE>
+<DL>
+<DD>Implements insertUpdate of <CODE>DocumentListener</CODE>
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>insertUpdate</CODE> in interface <CODE>javax.swing.event.DocumentListener</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeUpdate(javax.swing.event.DocumentEvent)"><!-- --></A><H3>
+removeUpdate</H3>
+<PRE>
+public void <B>removeUpdate</B>(javax.swing.event.DocumentEvent e)</PRE>
+<DL>
+<DD>Implements removeUpdate of <CODE>DocumentListener</CODE>
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>removeUpdate</CODE> in interface <CODE>javax.swing.event.DocumentListener</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changedUpdate(javax.swing.event.DocumentEvent)"><!-- --></A><H3>
+changedUpdate</H3>
+<PRE>
+public void <B>changedUpdate</B>(javax.swing.event.DocumentEvent e)</PRE>
+<DL>
+<DD>Implements changedUpdate of <CODE>DocumentListener</CODE>
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>changedUpdate</CODE> in interface <CODE>javax.swing.event.DocumentListener</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clipboardCheck(java.lang.String)"><!-- --></A><H3>
+clipboardCheck</H3>
+<PRE>
+public void <B>clipboardCheck</B>(java.lang.String clipboardContents)</PRE>
+<DL>
+<DD>Implements the notify method of the interface <A HREF="../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardListener</CODE></A>
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../jaligner/ui/clipboard/ClipboardListener.html#clipboardCheck(java.lang.String)">clipboardCheck</A></CODE> in interface <CODE><A HREF="../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>clipboardContents</CODE> - The current contents of the clipboard</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(java.lang.String[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - </DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignWindow.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignWindow.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/class-use/AlignCommandLine.html b/api/jaligner/ui/class-use/AlignCommandLine.html
new file mode 100644
index 0000000..2c64220
--- /dev/null
+++ b/api/jaligner/ui/class-use/AlignCommandLine.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.AlignCommandLine (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.AlignCommandLine (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignCommandLine.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.AlignCommandLine</B></H2>
+</CENTER>
+No usage of jaligner.ui.AlignCommandLine
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignCommandLine.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/class-use/AlignWindow.html b/api/jaligner/ui/class-use/AlignWindow.html
new file mode 100644
index 0000000..eddc952
--- /dev/null
+++ b/api/jaligner/ui/class-use/AlignWindow.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.AlignWindow (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.AlignWindow (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignWindow.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.AlignWindow</B></H2>
+</CENTER>
+No usage of jaligner.ui.AlignWindow
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="AlignWindow.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/ClipboardHandler.html b/api/jaligner/ui/clipboard/ClipboardHandler.html
new file mode 100644
index 0000000..4317186
--- /dev/null
+++ b/api/jaligner/ui/clipboard/ClipboardHandler.html
@@ -0,0 +1,248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ClipboardHandler (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard.ClipboardHandler interface">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ClipboardHandler (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandler.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.clipboard</FONT>
+<BR>
+Interface ClipboardHandler</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A>, <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ClipboardHandler</B></DL>
+
+<P>
+Abstract class to handle setting and getting "text" contents of
+ the system clipboard.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html#getContents()">getContents</A></B>()</CODE>
+
+<BR>
+ Returns the contents of the system of the clipboard</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html#setContents(java.lang.String)">setContents</A></B>(java.lang.String s)</CODE>
+
+<BR>
+ Sets the contents of the system of the clipboard</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getContents()"><!-- --></A><H3>
+getContents</H3>
+<PRE>
+public java.lang.String <B>getContents</B>()</PRE>
+<DL>
+<DD>Returns the contents of the system of the clipboard
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>String</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setContents(java.lang.String)"><!-- --></A><H3>
+setContents</H3>
+<PRE>
+public void <B>setContents</B>(java.lang.String s)</PRE>
+<DL>
+<DD>Sets the contents of the system of the clipboard
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>s</CODE> - the clipboard contents to set</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandler.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/ClipboardHandlerAWT.html b/api/jaligner/ui/clipboard/ClipboardHandlerAWT.html
new file mode 100644
index 0000000..788cfca
--- /dev/null
+++ b/api/jaligner/ui/clipboard/ClipboardHandlerAWT.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ClipboardHandlerAWT (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard.ClipboardHandlerAWT class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ClipboardHandlerAWT (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandlerAWT.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerAWT.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.clipboard</FONT>
+<BR>
+Class ClipboardHandlerAWT</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.clipboard.ClipboardHandlerAWT</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ClipboardHandlerAWT</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></DL>
+
+<P>
+Sets and gets the contents of the system clipboard.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html#ClipboardHandlerAWT()">ClipboardHandlerAWT</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html#getContents()">getContents</A></B>()</CODE>
+
+<BR>
+ Gets the contents of the system clipboard</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html#setContents(java.lang.String)">setContents</A></B>(java.lang.String s)</CODE>
+
+<BR>
+ Sets the contents of the system clipboard</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ClipboardHandlerAWT()"><!-- --></A><H3>
+ClipboardHandlerAWT</H3>
+<PRE>
+public <B>ClipboardHandlerAWT</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getContents()"><!-- --></A><H3>
+getContents</H3>
+<PRE>
+public java.lang.String <B>getContents</B>()</PRE>
+<DL>
+<DD>Gets the contents of the system clipboard
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html#getContents()">getContents</A></CODE> in interface <CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>The text contents of the system clipboard</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setContents(java.lang.String)"><!-- --></A><H3>
+setContents</H3>
+<PRE>
+public void <B>setContents</B>(java.lang.String s)</PRE>
+<DL>
+<DD>Sets the contents of the system clipboard
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html#setContents(java.lang.String)">setContents</A></CODE> in interface <CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>s</CODE> - the clipboard contents to set</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandlerAWT.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerAWT.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/ClipboardHandlerFactory.html b/api/jaligner/ui/clipboard/ClipboardHandlerFactory.html
new file mode 100644
index 0000000..72bc1a3
--- /dev/null
+++ b/api/jaligner/ui/clipboard/ClipboardHandlerFactory.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ClipboardHandlerFactory (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard.ClipboardHandlerFactory class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ClipboardHandlerFactory (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandlerFactory.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.clipboard</FONT>
+<BR>
+Class ClipboardHandlerFactory</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.clipboard.ClipboardHandlerFactory</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ClipboardHandlerFactory</B><DT>extends java.lang.Object</DL>
+
+<P>
+A factory for <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html#getClipboardHandler()">getClipboardHandler</A></B>()</CODE>
+
+<BR>
+ Returns an instance of a concrete <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getClipboardHandler()"><!-- --></A><H3>
+getClipboardHandler</H3>
+<PRE>
+public static <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A> <B>getClipboardHandler</B>()</PRE>
+<DL>
+<DD>Returns an instance of a concrete <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Concrete <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandlerFactory.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/ClipboardHandlerJNLP.html b/api/jaligner/ui/clipboard/ClipboardHandlerJNLP.html
new file mode 100644
index 0000000..d00caa3
--- /dev/null
+++ b/api/jaligner/ui/clipboard/ClipboardHandlerJNLP.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ClipboardHandlerJNLP (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard.ClipboardHandlerJNLP class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ClipboardHandlerJNLP (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandlerJNLP.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.clipboard</FONT>
+<BR>
+Class ClipboardHandlerJNLP</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.clipboard.ClipboardHandlerJNLP</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ClipboardHandlerJNLP</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></DL>
+
+<P>
+Sets and gets the contents of the system clipboard.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html#ClipboardHandlerJNLP()">ClipboardHandlerJNLP</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html#getContents()">getContents</A></B>()</CODE>
+
+<BR>
+ Gets the contents of the system clipboard</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html#setContents(java.lang.String)">setContents</A></B>(java.lang.String s)</CODE>
+
+<BR>
+ Sets the contents of the system clipboard</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ClipboardHandlerJNLP()"><!-- --></A><H3>
+ClipboardHandlerJNLP</H3>
+<PRE>
+public <B>ClipboardHandlerJNLP</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getContents()"><!-- --></A><H3>
+getContents</H3>
+<PRE>
+public java.lang.String <B>getContents</B>()</PRE>
+<DL>
+<DD>Gets the contents of the system clipboard
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html#getContents()">getContents</A></CODE> in interface <CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>The text system clipboad contents</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setContents(java.lang.String)"><!-- --></A><H3>
+setContents</H3>
+<PRE>
+public void <B>setContents</B>(java.lang.String s)</PRE>
+<DL>
+<DD>Sets the contents of the system clipboard
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html#setContents(java.lang.String)">setContents</A></CODE> in interface <CODE><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>s</CODE> - clipboard contents to set</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardHandlerJNLP.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/ClipboardListener.html b/api/jaligner/ui/clipboard/ClipboardListener.html
new file mode 100644
index 0000000..f3876af
--- /dev/null
+++ b/api/jaligner/ui/clipboard/ClipboardListener.html
@@ -0,0 +1,225 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ClipboardListener (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard.ClipboardListener interface">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ClipboardListener (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardListener.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardListener.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.clipboard</FONT>
+<BR>
+Interface ClipboardListener</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ClipboardListener</B></DL>
+
+<P>
+Listener interface to get notified with the clipboard contents.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html#clipboardCheck(java.lang.String)">clipboardCheck</A></B>(java.lang.String contents)</CODE>
+
+<BR>
+ Notifies the listener with the current contents of the clipboard.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="clipboardCheck(java.lang.String)"><!-- --></A><H3>
+clipboardCheck</H3>
+<PRE>
+public void <B>clipboardCheck</B>(java.lang.String contents)</PRE>
+<DL>
+<DD>Notifies the listener with the current contents of the clipboard.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>contents</CODE> - The current contents of the clipboard</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardListener.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardListener.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/ClipboardPoller.html b/api/jaligner/ui/clipboard/ClipboardPoller.html
new file mode 100644
index 0000000..8a2d0c9
--- /dev/null
+++ b/api/jaligner/ui/clipboard/ClipboardPoller.html
@@ -0,0 +1,314 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ClipboardPoller (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard.ClipboardPoller class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ClipboardPoller (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardPoller.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardPoller.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.lang.Thread">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.clipboard</FONT>
+<BR>
+Class ClipboardPoller</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.lang.Thread
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.clipboard.ClipboardPoller</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.lang.Runnable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ClipboardPoller</B><DT>extends java.lang.Thread</DL>
+
+<P>
+Checks the system clipboard to notifies a listener with current contents.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.lang.Thread"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.lang.Thread</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY</CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html#ClipboardPoller(jaligner.ui.clipboard.ClipboardListener)">ClipboardPoller</A></B>(<A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A> listener)</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html#run()">run</A></B>()</CODE>
+
+<BR>
+ Runs the thread</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html#start()">start</A></B>()</CODE>
+
+<BR>
+ Starts the thread</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Thread"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Thread</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getContextClassLoader, getName, getPriority, getThreadGroup, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setName, setPriority, sleep, sleep, stop, stop, suspend, toString, yield</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ClipboardPoller(jaligner.ui.clipboard.ClipboardListener)"><!-- --></A><H3>
+ClipboardPoller</H3>
+<PRE>
+public <B>ClipboardPoller</B>(<A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A> listener)</PRE>
+<DL>
+<DD>Constructor
+<P>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="run()"><!-- --></A><H3>
+run</H3>
+<PRE>
+public void <B>run</B>()</PRE>
+<DL>
+<DD>Runs the thread
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD>Starts the thread
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClipboardPoller.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardPoller.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.lang.Thread">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/class-use/ClipboardHandler.html b/api/jaligner/ui/clipboard/class-use/ClipboardHandler.html
new file mode 100644
index 0000000..5f6d823
--- /dev/null
+++ b/api/jaligner/ui/clipboard/class-use/ClipboardHandler.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Interface jaligner.ui.clipboard.ClipboardHandler (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Interface jaligner.ui.clipboard.ClipboardHandler (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Interface<br>jaligner.ui.clipboard.ClipboardHandler</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.clipboard"><B>jaligner.ui.clipboard</B></A></TD>
+<TD>Clipboard handling for JNLP and AWT. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.clipboard"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A> in <A HREF="../../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Classes in <A HREF="../../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A> that implement <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A></B></CODE>
+
+<BR>
+ Sets and gets the contents of the system clipboard.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A></B></CODE>
+
+<BR>
+ Sets and gets the contents of the system clipboard.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A> that return <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></CODE></FONT></TD>
+<TD><CODE><B>ClipboardHandlerFactory.</B><B><A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html#getClipboardHandler()">getClipboardHandler</A></B>()</CODE>
+
+<BR>
+ Returns an instance of a concrete <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/class-use/ClipboardHandlerAWT.html b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerAWT.html
new file mode 100644
index 0000000..184085e
--- /dev/null
+++ b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerAWT.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.clipboard.ClipboardHandlerAWT (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.clipboard.ClipboardHandlerAWT (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerAWT.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.clipboard.ClipboardHandlerAWT</B></H2>
+</CENTER>
+No usage of jaligner.ui.clipboard.ClipboardHandlerAWT
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerAWT.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/class-use/ClipboardHandlerFactory.html b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerFactory.html
new file mode 100644
index 0000000..40a9a41
--- /dev/null
+++ b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerFactory.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.clipboard.ClipboardHandlerFactory (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.clipboard.ClipboardHandlerFactory (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.clipboard.ClipboardHandlerFactory</B></H2>
+</CENTER>
+No usage of jaligner.ui.clipboard.ClipboardHandlerFactory
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/class-use/ClipboardHandlerJNLP.html b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerJNLP.html
new file mode 100644
index 0000000..9d11863
--- /dev/null
+++ b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerJNLP.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.clipboard.ClipboardHandlerJNLP (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.clipboard.ClipboardHandlerJNLP (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.clipboard.ClipboardHandlerJNLP</B></H2>
+</CENTER>
+No usage of jaligner.ui.clipboard.ClipboardHandlerJNLP
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardHandlerJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/class-use/ClipboardListener.html b/api/jaligner/ui/clipboard/class-use/ClipboardListener.html
new file mode 100644
index 0000000..e96f0eb
--- /dev/null
+++ b/api/jaligner/ui/clipboard/class-use/ClipboardListener.html
@@ -0,0 +1,199 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Interface jaligner.ui.clipboard.ClipboardListener (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Interface jaligner.ui.clipboard.ClipboardListener (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardListener.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Interface<br>jaligner.ui.clipboard.ClipboardListener</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui"><B>jaligner.ui</B></A></TD>
+<TD>Command line and graphical user interface. </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.clipboard"><B>jaligner.ui.clipboard</B></A></TD>
+<TD>Clipboard handling for JNLP and AWT. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A> in <A HREF="../../../../jaligner/ui/package-summary.html">jaligner.ui</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Classes in <A HREF="../../../../jaligner/ui/package-summary.html">jaligner.ui</A> that implement <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A></B></CODE>
+
+<BR>
+ Graphical user inteface for JAligner.</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.clipboard"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A> in <A HREF="../../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Constructors in <A HREF="../../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A> with parameters of type <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../jaligner/ui/clipboard/ClipboardPoller.html#ClipboardPoller(jaligner.ui.clipboard.ClipboardListener)">ClipboardPoller</A></B>(<A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A> listener)</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardListener.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/class-use/ClipboardPoller.html b/api/jaligner/ui/clipboard/class-use/ClipboardPoller.html
new file mode 100644
index 0000000..4838e8f
--- /dev/null
+++ b/api/jaligner/ui/clipboard/class-use/ClipboardPoller.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.clipboard.ClipboardPoller (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.clipboard.ClipboardPoller (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardPoller.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.clipboard.ClipboardPoller</B></H2>
+</CENTER>
+No usage of jaligner.ui.clipboard.ClipboardPoller
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ClipboardPoller.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/package-frame.html b/api/jaligner/ui/clipboard/package-frame.html
new file mode 100644
index 0000000..ede0c46
--- /dev/null
+++ b/api/jaligner/ui/clipboard/package-frame.html
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.clipboard (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../jaligner/ui/clipboard/package-summary.html" target="classFrame">jaligner.ui.clipboard</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ClipboardHandler.html" title="interface in jaligner.ui.clipboard" target="classFrame"><I>ClipboardHandler</I></A>
+<BR>
+<A HREF="ClipboardListener.html" title="interface in jaligner.ui.clipboard" target="classFrame"><I>ClipboardListener</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardHandlerAWT</A>
+<BR>
+<A HREF="ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardHandlerFactory</A>
+<BR>
+<A HREF="ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardHandlerJNLP</A>
+<BR>
+<A HREF="ClipboardPoller.html" title="class in jaligner.ui.clipboard" target="classFrame">ClipboardPoller</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/package-summary.html b/api/jaligner/ui/clipboard/package-summary.html
new file mode 100644
index 0000000..761e691
--- /dev/null
+++ b/api/jaligner/ui/clipboard/package-summary.html
@@ -0,0 +1,198 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.clipboard (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.clipboard package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.clipboard (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.ui.clipboard
+</H2>
+Clipboard handling for JNLP and AWT.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A></B></TD>
+<TD>Abstract class to handle setting and getting "text" contents of
+ the system clipboard.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A></B></TD>
+<TD>Listener interface to get notified with the clipboard contents.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard">ClipboardHandlerAWT</A></B></TD>
+<TD>Sets and gets the contents of the system clipboard.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard">ClipboardHandlerFactory</A></B></TD>
+<TD>A factory for <A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><CODE>ClipboardHandler</CODE></A>.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard">ClipboardHandlerJNLP</A></B></TD>
+<TD>Sets and gets the contents of the system clipboard.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard">ClipboardPoller</A></B></TD>
+<TD>Checks the system clipboard to notifies a listener with current contents.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.ui.clipboard Description
+</H2>
+
+<P>
+Clipboard handling for JNLP and AWT.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/package-tree.html b/api/jaligner/ui/clipboard/package-tree.html
new file mode 100644
index 0000000..df3711f
--- /dev/null
+++ b/api/jaligner/ui/clipboard/package-tree.html
@@ -0,0 +1,155 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.clipboard Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.clipboard Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.ui.clipboard
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerAWT.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerAWT</B></A> (implements jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">ClipboardHandler</A>)
+<LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerFactory</B></A><LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerJNLP</B></A> (implements jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in ja [...]
+<LI TYPE="circle">class java.lang.Thread (implements java.lang.Runnable)
+<UL>
+<LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><B>ClipboardPoller</B></A></UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><B>ClipboardHandler</B></A><LI TYPE="circle">interface jaligner.ui.clipboard.<A HREF="../../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><B>ClipboardListener</B></A></UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/clipboard/package-use.html b/api/jaligner/ui/clipboard/package-use.html
new file mode 100644
index 0000000..1b9ad65
--- /dev/null
+++ b/api/jaligner/ui/clipboard/package-use.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.ui.clipboard (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.ui.clipboard (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.ui.clipboard</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui"><B>jaligner.ui</B></A></TD>
+<TD>Command line and graphical user interface. </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.clipboard"><B>jaligner.ui.clipboard</B></A></TD>
+<TD>Clipboard handling for JNLP and AWT. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A> used by <A HREF="../../../jaligner/ui/package-summary.html">jaligner.ui</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/clipboard/class-use/ClipboardListener.html#jaligner.ui"><B>ClipboardListener</B></A></B>
+
+<BR>
+ Listener interface to get notified with the clipboard contents.</TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.clipboard"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A> used by <A HREF="../../../jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/clipboard/class-use/ClipboardHandler.html#jaligner.ui.clipboard"><B>ClipboardHandler</B></A></B>
+
+<BR>
+ Abstract class to handle setting and getting "text" contents of
+ the system clipboard.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/clipboard/class-use/ClipboardListener.html#jaligner.ui.clipboard"><B>ClipboardListener</B></A></B>
+
+<BR>
+ Listener interface to get notified with the clipboard contents.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/FileChooser.html b/api/jaligner/ui/filechooser/FileChooser.html
new file mode 100644
index 0000000..9805838
--- /dev/null
+++ b/api/jaligner/ui/filechooser/FileChooser.html
@@ -0,0 +1,372 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FileChooser (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser.FileChooser class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FileChooser (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooser.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.filechooser</FONT>
+<BR>
+Class FileChooser</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.filechooser.FileChooser</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A>, <A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>FileChooser</B><DT>extends java.lang.Object</DL>
+
+<P>
+Opens and saves files.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#BUFFER_SIZE">BUFFER_SIZE</A></B></CODE>
+
+<BR>
+ Buffer size while reading from or write to a file (4 KB)</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#FileChooser()">FileChooser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#getUserDirectory()">getUserDirectory</A></B>()</CODE>
+
+<BR>
+ Gets the current user working directory</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#save(java.io.InputStream, java.lang.String)">save</A></B>(java.io.InputStream is,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves an input stream to a file</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#setUserDirectory(java.lang.String)">setUserDirectory</A></B>(java.lang.String userDir)</CODE>
+
+<BR>
+ Sets the user working directory</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BUFFER_SIZE"><!-- --></A><H3>
+BUFFER_SIZE</H3>
+<PRE>
+public static final int <B>BUFFER_SIZE</B></PRE>
+<DL>
+<DD>Buffer size while reading from or write to a file (4 KB)
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#jaligner.ui.filechooser.FileChooser.BUFFER_SIZE">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileChooser()"><!-- --></A><H3>
+FileChooser</H3>
+<PRE>
+public <B>FileChooser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="open()"><!-- --></A><H3>
+open</H3>
+<PRE>
+public abstract <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> <B>open</B>()
+ throws <A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></PRE>
+<DL>
+<DD>Shows a dialog to select a file
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>InputStream
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="save(java.io.InputStream, java.lang.String)"><!-- --></A><H3>
+save</H3>
+<PRE>
+public abstract boolean <B>save</B>(java.io.InputStream is,
+ java.lang.String fileName)
+ throws <A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></PRE>
+<DL>
+<DD>Saves an input stream to a file
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>is</CODE> - <DD><CODE>fileName</CODE> -
+<DT><B>Returns:</B><DD>boolean
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUserDirectory()"><!-- --></A><H3>
+getUserDirectory</H3>
+<PRE>
+public java.lang.String <B>getUserDirectory</B>()</PRE>
+<DL>
+<DD>Gets the current user working directory
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>current working directory</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setUserDirectory(java.lang.String)"><!-- --></A><H3>
+setUserDirectory</H3>
+<PRE>
+public void <B>setUserDirectory</B>(java.lang.String userDir)</PRE>
+<DL>
+<DD>Sets the user working directory
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>userDir</CODE> - The user directory to set</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooser.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/FileChooserException.html b/api/jaligner/ui/filechooser/FileChooserException.html
new file mode 100644
index 0000000..87e22df
--- /dev/null
+++ b/api/jaligner/ui/filechooser/FileChooserException.html
@@ -0,0 +1,242 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FileChooserException (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser.FileChooserException class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FileChooserException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.filechooser</FONT>
+<BR>
+Class FileChooserException</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.lang.Throwable
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.lang.Exception
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.filechooser.FileChooserException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileChooserException</B><DT>extends java.lang.Exception</DL>
+
+<P>
+File chooser exception
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../serialized-form.html#jaligner.ui.filechooser.FileChooserException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html#FileChooserException(java.lang.String)">FileChooserException</A></B>(java.lang.String message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Throwable</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileChooserException(java.lang.String)"><!-- --></A><H3>
+FileChooserException</H3>
+<PRE>
+public <B>FileChooserException</B>(java.lang.String message)</PRE>
+<DL>
+<DT><B>Parameters:</B><DD><CODE>message</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/FileChooserFactory.html b/api/jaligner/ui/filechooser/FileChooserFactory.html
new file mode 100644
index 0000000..bc355d2
--- /dev/null
+++ b/api/jaligner/ui/filechooser/FileChooserFactory.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FileChooserFactory (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser.FileChooserFactory class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FileChooserFactory (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserFactory.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.filechooser</FONT>
+<BR>
+Class FileChooserFactory</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.filechooser.FileChooserFactory</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>FileChooserFactory</B><DT>extends java.lang.Object</DL>
+
+<P>
+A factory for <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html#getFileChooser()">getFileChooser</A></B>()</CODE>
+
+<BR>
+ Returns an instance of a concrete <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFileChooser()"><!-- --></A><H3>
+getFileChooser</H3>
+<PRE>
+public static <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A> <B>getFileChooser</B>()</PRE>
+<DL>
+<DD>Returns an instance of a concrete <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Concrete <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserFactory.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/FileChooserJNLP.html b/api/jaligner/ui/filechooser/FileChooserJNLP.html
new file mode 100644
index 0000000..ee9ca87
--- /dev/null
+++ b/api/jaligner/ui/filechooser/FileChooserJNLP.html
@@ -0,0 +1,325 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FileChooserJNLP (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser.FileChooserJNLP class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FileChooserJNLP (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserJNLP.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_jaligner.ui.filechooser.FileChooser">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.filechooser</FONT>
+<BR>
+Class FileChooserJNLP</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">jaligner.ui.filechooser.FileChooser</A>
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.filechooser.FileChooserJNLP</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>FileChooserJNLP</B><DT>extends <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></DL>
+
+<P>
+Opens and saves files.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_jaligner.ui.filechooser.FileChooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#BUFFER_SIZE">BUFFER_SIZE</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html#FileChooserJNLP()">FileChooserJNLP</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html#save(java.io.InputStream, java.lang.String)">save</A></B>(java.io.InputStream is,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves an input stream to a file.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_jaligner.ui.filechooser.FileChooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#getUserDirectory()">getUserDirectory</A>, <A HREF="../../../jaligner/ui/filechooser/FileChooser.html#setUserDirectory(java.lang.String)">setUserDirectory</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileChooserJNLP()"><!-- --></A><H3>
+FileChooserJNLP</H3>
+<PRE>
+public <B>FileChooserJNLP</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="open()"><!-- --></A><H3>
+open</H3>
+<PRE>
+public <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> <B>open</B>()
+ throws <A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></PRE>
+<DL>
+<DD>Shows a dialog to select a file.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#open()">open</A></CODE> in class <CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>InputStream
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="save(java.io.InputStream, java.lang.String)"><!-- --></A><H3>
+save</H3>
+<PRE>
+public boolean <B>save</B>(java.io.InputStream is,
+ java.lang.String fileName)
+ throws <A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></PRE>
+<DL>
+<DD>Saves an input stream to a file.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#save(java.io.InputStream, java.lang.String)">save</A></CODE> in class <CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>is</CODE> - <DD><CODE>fileName</CODE> -
+<DT><B>Returns:</B><DD>Boolean
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserJNLP.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_jaligner.ui.filechooser.FileChooser">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/FileChooserTrusted.html b/api/jaligner/ui/filechooser/FileChooserTrusted.html
new file mode 100644
index 0000000..d15bb5e
--- /dev/null
+++ b/api/jaligner/ui/filechooser/FileChooserTrusted.html
@@ -0,0 +1,325 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+FileChooserTrusted (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser.FileChooserTrusted class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="FileChooserTrusted (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserTrusted.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserTrusted.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_jaligner.ui.filechooser.FileChooser">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.filechooser</FONT>
+<BR>
+Class FileChooserTrusted</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">jaligner.ui.filechooser.FileChooser</A>
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.filechooser.FileChooserTrusted</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>FileChooserTrusted</B><DT>extends <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></DL>
+
+<P>
+Opens and saves files.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_jaligner.ui.filechooser.FileChooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#BUFFER_SIZE">BUFFER_SIZE</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html#FileChooserTrusted()">FileChooserTrusted</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html#save(java.io.InputStream, java.lang.String)">save</A></B>(java.io.InputStream is,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves an input stream to a file.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_jaligner.ui.filechooser.FileChooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#getUserDirectory()">getUserDirectory</A>, <A HREF="../../../jaligner/ui/filechooser/FileChooser.html#setUserDirectory(java.lang.String)">setUserDirectory</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileChooserTrusted()"><!-- --></A><H3>
+FileChooserTrusted</H3>
+<PRE>
+public <B>FileChooserTrusted</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="open()"><!-- --></A><H3>
+open</H3>
+<PRE>
+public <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> <B>open</B>()
+ throws <A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></PRE>
+<DL>
+<DD>Shows a dialog to select a file.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#open()">open</A></CODE> in class <CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>input stream
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><CODE>NamedInputStream</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="save(java.io.InputStream, java.lang.String)"><!-- --></A><H3>
+save</H3>
+<PRE>
+public boolean <B>save</B>(java.io.InputStream is,
+ java.lang.String fileName)
+ throws <A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></PRE>
+<DL>
+<DD>Saves an input stream to a file.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html#save(java.io.InputStream, java.lang.String)">save</A></CODE> in class <CODE><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>is</CODE> - <DD><CODE>fileName</CODE> -
+<DT><B>Returns:</B><DD>boolean
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FileChooserTrusted.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ <A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserTrusted.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_jaligner.ui.filechooser.FileChooser">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/NamedInputStream.html b/api/jaligner/ui/filechooser/NamedInputStream.html
new file mode 100644
index 0000000..8fa6ff3
--- /dev/null
+++ b/api/jaligner/ui/filechooser/NamedInputStream.html
@@ -0,0 +1,288 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+NamedInputStream (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser.NamedInputStream class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="NamedInputStream (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/NamedInputStream.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="NamedInputStream.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.filechooser</FONT>
+<BR>
+Class NamedInputStream</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.filechooser.NamedInputStream</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NamedInputStream</B><DT>extends java.lang.Object<DT>implements java.io.Serializable</DL>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../serialized-form.html#jaligner.ui.filechooser.NamedInputStream">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html#NamedInputStream(java.lang.String, java.io.InputStream)">NamedInputStream</A></B>(java.lang.String name,
+ java.io.InputStream inputStream)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.io.InputStream</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html#getInputStream()">getInputStream</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NamedInputStream(java.lang.String, java.io.InputStream)"><!-- --></A><H3>
+NamedInputStream</H3>
+<PRE>
+public <B>NamedInputStream</B>(java.lang.String name,
+ java.io.InputStream inputStream)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInputStream()"><!-- --></A><H3>
+getInputStream</H3>
+<PRE>
+public java.io.InputStream <B>getInputStream</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the inputStream.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public java.lang.String <B>getName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Returns the name.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/NamedInputStream.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="NamedInputStream.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/class-use/FileChooser.html b/api/jaligner/ui/filechooser/class-use/FileChooser.html
new file mode 100644
index 0000000..509f76b
--- /dev/null
+++ b/api/jaligner/ui/filechooser/class-use/FileChooser.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.filechooser.FileChooser (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.filechooser.FileChooser (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooser.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.filechooser.FileChooser</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.filechooser"><B>jaligner.ui.filechooser</B></A></TD>
+<TD>File loading and storing. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.filechooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A> in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Subclasses of <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A> in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A></B></CODE>
+
+<BR>
+ Opens and saves files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A></B></CODE>
+
+<BR>
+ Opens and saves files.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A> that return <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooserFactory.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserFactory.html#getFileChooser()">getFileChooser</A></B>()</CODE>
+
+<BR>
+ Returns an instance of a concrete <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooser.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/class-use/FileChooserException.html b/api/jaligner/ui/filechooser/class-use/FileChooserException.html
new file mode 100644
index 0000000..3af6a3b
--- /dev/null
+++ b/api/jaligner/ui/filechooser/class-use/FileChooserException.html
@@ -0,0 +1,215 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.filechooser.FileChooserException (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.filechooser.FileChooserException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.filechooser.FileChooserException</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.filechooser"><B>jaligner.ui.filechooser</B></A></TD>
+<TD>File loading and storing. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.filechooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A> in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A> that throw <A HREF="../../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooserTrusted.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserTrusted.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B>FileChooserTrusted.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserTrusted.html#save(java.io.InputStream, java.lang.String)">save</A></B>(java.io.InputStream is,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves an input stream to a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooserJNLP.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserJNLP.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B>FileChooserJNLP.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserJNLP.html#save(java.io.InputStream, java.lang.String)">save</A></B>(java.io.InputStream is,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves an input stream to a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooser.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooser.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract boolean</CODE></FONT></TD>
+<TD><CODE><B>FileChooser.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooser.html#save(java.io.InputStream, java.lang.String)">save</A></B>(java.io.InputStream is,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves an input stream to a file</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/class-use/FileChooserFactory.html b/api/jaligner/ui/filechooser/class-use/FileChooserFactory.html
new file mode 100644
index 0000000..2fe5870
--- /dev/null
+++ b/api/jaligner/ui/filechooser/class-use/FileChooserFactory.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.filechooser.FileChooserFactory (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.filechooser.FileChooserFactory (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.filechooser.FileChooserFactory</B></H2>
+</CENTER>
+No usage of jaligner.ui.filechooser.FileChooserFactory
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserFactory.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/class-use/FileChooserJNLP.html b/api/jaligner/ui/filechooser/class-use/FileChooserJNLP.html
new file mode 100644
index 0000000..86c4642
--- /dev/null
+++ b/api/jaligner/ui/filechooser/class-use/FileChooserJNLP.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.filechooser.FileChooserJNLP (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.filechooser.FileChooserJNLP (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.filechooser.FileChooserJNLP</B></H2>
+</CENTER>
+No usage of jaligner.ui.filechooser.FileChooserJNLP
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserJNLP.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/class-use/FileChooserTrusted.html b/api/jaligner/ui/filechooser/class-use/FileChooserTrusted.html
new file mode 100644
index 0000000..bbb4eab
--- /dev/null
+++ b/api/jaligner/ui/filechooser/class-use/FileChooserTrusted.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.filechooser.FileChooserTrusted (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.filechooser.FileChooserTrusted (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserTrusted.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.filechooser.FileChooserTrusted</B></H2>
+</CENTER>
+No usage of jaligner.ui.filechooser.FileChooserTrusted
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="FileChooserTrusted.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/class-use/NamedInputStream.html b/api/jaligner/ui/filechooser/class-use/NamedInputStream.html
new file mode 100644
index 0000000..6f5aed1
--- /dev/null
+++ b/api/jaligner/ui/filechooser/class-use/NamedInputStream.html
@@ -0,0 +1,217 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.filechooser.NamedInputStream (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.filechooser.NamedInputStream (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="NamedInputStream.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.filechooser.NamedInputStream</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.matrix"><B>jaligner.matrix</B></A></TD>
+<TD>Scoring matrices package. </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.filechooser"><B>jaligner.ui.filechooser</B></A></TD>
+<TD>File loading and storing. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.matrix"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> in <A HREF="../../../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../../jaligner/matrix/package-summary.html">jaligner.matrix</A> with parameters of type <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../jaligner/matrix/Matrix.html" title="class in jaligner.matrix">Matrix</A></CODE></FONT></TD>
+<TD><CODE><B>MatrixLoader.</B><B><A HREF="../../../../jaligner/matrix/MatrixLoader.html#load(jaligner.ui.filechooser.NamedInputStream)">load</A></B>(<A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> nis)</CODE>
+
+<BR>
+ Loads scoring matrix from <CODE>InputStream</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.filechooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A> in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A> that return <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooserTrusted.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserTrusted.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooserJNLP.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooserJNLP.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></CODE></FONT></TD>
+<TD><CODE><B>FileChooser.</B><B><A HREF="../../../../jaligner/ui/filechooser/FileChooser.html#open()">open</A></B>()</CODE>
+
+<BR>
+ Shows a dialog to select a file</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="NamedInputStream.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/package-frame.html b/api/jaligner/ui/filechooser/package-frame.html
new file mode 100644
index 0000000..d3bd8e4
--- /dev/null
+++ b/api/jaligner/ui/filechooser/package-frame.html
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.filechooser (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../jaligner/ui/filechooser/package-summary.html" target="classFrame">jaligner.ui.filechooser</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="FileChooser.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooser</A>
+<BR>
+<A HREF="FileChooserFactory.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserFactory</A>
+<BR>
+<A HREF="FileChooserJNLP.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserJNLP</A>
+<BR>
+<A HREF="FileChooserTrusted.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserTrusted</A>
+<BR>
+<A HREF="NamedInputStream.html" title="class in jaligner.ui.filechooser" target="classFrame">NamedInputStream</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="FileChooserException.html" title="class in jaligner.ui.filechooser" target="classFrame">FileChooserException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/package-summary.html b/api/jaligner/ui/filechooser/package-summary.html
new file mode 100644
index 0000000..098aacb
--- /dev/null
+++ b/api/jaligner/ui/filechooser/package-summary.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.filechooser (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.filechooser package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.filechooser (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/images/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.ui.filechooser
+</H2>
+File loading and storing.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser">FileChooser</A></B></TD>
+<TD>Opens and saves files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser">FileChooserFactory</A></B></TD>
+<TD>A factory for <A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><CODE>FileChooser</CODE></A>.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser">FileChooserJNLP</A></B></TD>
+<TD>Opens and saves files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser">FileChooserTrusted</A></B></TD>
+<TD>Opens and saves files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">NamedInputStream</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">FileChooserException</A></B></TD>
+<TD>File chooser exception</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.ui.filechooser Description
+</H2>
+
+<P>
+File loading and storing.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/images/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/package-tree.html b/api/jaligner/ui/filechooser/package-tree.html
new file mode 100644
index 0000000..1507051
--- /dev/null
+++ b/api/jaligner/ui/filechooser/package-tree.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.filechooser Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.filechooser Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/images/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.ui.filechooser
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><B>FileChooser</B></A><UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><B>FileChooserJNLP</B></A><LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>FileChooserTrusted</B></A></UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>FileChooserFactory</B></A><LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><B>NamedInputStream</B></A> (implements java.io.Serializable)
+<LI TYPE="circle">class java.lang.Throwable (implements java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.lang.Exception<UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="../../../jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser"><B>FileChooserException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/clipboard/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/images/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/filechooser/package-use.html b/api/jaligner/ui/filechooser/package-use.html
new file mode 100644
index 0000000..d4f3d26
--- /dev/null
+++ b/api/jaligner/ui/filechooser/package-use.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.ui.filechooser (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.ui.filechooser (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.ui.filechooser</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.matrix"><B>jaligner.matrix</B></A></TD>
+<TD>Scoring matrices package. </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.filechooser"><B>jaligner.ui.filechooser</B></A></TD>
+<TD>File loading and storing. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.matrix"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A> used by <A HREF="../../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/filechooser/class-use/NamedInputStream.html#jaligner.matrix"><B>NamedInputStream</B></A></B>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.filechooser"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A> used by <A HREF="../../../jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/filechooser/class-use/FileChooser.html#jaligner.ui.filechooser"><B>FileChooser</B></A></B>
+
+<BR>
+ Opens and saves files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/filechooser/class-use/FileChooserException.html#jaligner.ui.filechooser"><B>FileChooserException</B></A></B>
+
+<BR>
+ File chooser exception</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/filechooser/class-use/NamedInputStream.html#jaligner.ui.filechooser"><B>NamedInputStream</B></A></B>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/images/ToolbarIcons.html b/api/jaligner/ui/images/ToolbarIcons.html
new file mode 100644
index 0000000..6d27da6
--- /dev/null
+++ b/api/jaligner/ui/images/ToolbarIcons.html
@@ -0,0 +1,441 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+ToolbarIcons (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.images.ToolbarIcons class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="ToolbarIcons (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ToolbarIcons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ToolbarIcons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.images</FONT>
+<BR>
+Class ToolbarIcons</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.images.ToolbarIcons</B>
+</PRE>
+<HR>
+<DL>
+<DT>public abstract class <B>ToolbarIcons</B><DT>extends java.lang.Object</DL>
+
+<P>
+Toolbar icons
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#ABOUT">ABOUT</A></B></CODE>
+
+<BR>
+ About icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#CLOSE">CLOSE</A></B></CODE>
+
+<BR>
+ Close icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#COPY">COPY</A></B></CODE>
+
+<BR>
+ Copy icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#CUT">CUT</A></B></CODE>
+
+<BR>
+ Cut icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#DELETE">DELETE</A></B></CODE>
+
+<BR>
+ Delete icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#GIFS_HOME">GIFS_HOME</A></B></CODE>
+
+<BR>
+ Path to the gifs folder</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#OPEN">OPEN</A></B></CODE>
+
+<BR>
+ Open icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#PASTE">PASTE</A></B></CODE>
+
+<BR>
+ Paste icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#PRINT">PRINT</A></B></CODE>
+
+<BR>
+ Print icon</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static javax.swing.ImageIcon</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#SAVE">SAVE</A></B></CODE>
+
+<BR>
+ Save icon</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html#ToolbarIcons()">ToolbarIcons</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GIFS_HOME"><!-- --></A><H3>
+GIFS_HOME</H3>
+<PRE>
+public static final java.lang.String <B>GIFS_HOME</B></PRE>
+<DL>
+<DD>Path to the gifs folder
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#jaligner.ui.images.ToolbarIcons.GIFS_HOME">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="OPEN"><!-- --></A><H3>
+OPEN</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>OPEN</B></PRE>
+<DL>
+<DD>Open icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="SAVE"><!-- --></A><H3>
+SAVE</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>SAVE</B></PRE>
+<DL>
+<DD>Save icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CUT"><!-- --></A><H3>
+CUT</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>CUT</B></PRE>
+<DL>
+<DD>Cut icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="COPY"><!-- --></A><H3>
+COPY</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>COPY</B></PRE>
+<DL>
+<DD>Copy icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="PASTE"><!-- --></A><H3>
+PASTE</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>PASTE</B></PRE>
+<DL>
+<DD>Paste icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="DELETE"><!-- --></A><H3>
+DELETE</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>DELETE</B></PRE>
+<DL>
+<DD>Delete icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CLOSE"><!-- --></A><H3>
+CLOSE</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>CLOSE</B></PRE>
+<DL>
+<DD>Close icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ABOUT"><!-- --></A><H3>
+ABOUT</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>ABOUT</B></PRE>
+<DL>
+<DD>About icon
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="PRINT"><!-- --></A><H3>
+PRINT</H3>
+<PRE>
+public static final javax.swing.ImageIcon <B>PRINT</B></PRE>
+<DL>
+<DD>Print icon
+<P>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ToolbarIcons()"><!-- --></A><H3>
+ToolbarIcons</H3>
+<PRE>
+public <B>ToolbarIcons</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ToolbarIcons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ToolbarIcons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/images/class-use/ToolbarIcons.html b/api/jaligner/ui/images/class-use/ToolbarIcons.html
new file mode 100644
index 0000000..7d24619
--- /dev/null
+++ b/api/jaligner/ui/images/class-use/ToolbarIcons.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.images.ToolbarIcons (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.images.ToolbarIcons (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ToolbarIcons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.images.ToolbarIcons</B></H2>
+</CENTER>
+No usage of jaligner.ui.images.ToolbarIcons
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="ToolbarIcons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/images/package-frame.html b/api/jaligner/ui/images/package-frame.html
new file mode 100644
index 0000000..e73580e
--- /dev/null
+++ b/api/jaligner/ui/images/package-frame.html
@@ -0,0 +1,32 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.images (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.images package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../jaligner/ui/images/package-summary.html" target="classFrame">jaligner.ui.images</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ToolbarIcons.html" title="class in jaligner.ui.images" target="classFrame">ToolbarIcons</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/images/package-summary.html b/api/jaligner/ui/images/package-summary.html
new file mode 100644
index 0000000..14e8da4
--- /dev/null
+++ b/api/jaligner/ui/images/package-summary.html
@@ -0,0 +1,167 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.images (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.images package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.images (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/logging/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.ui.images
+</H2>
+Images used in the toolbar.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images">ToolbarIcons</A></B></TD>
+<TD>Toolbar icons</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.ui.images Description
+</H2>
+
+<P>
+Images used in the toolbar.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/logging/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/images/package-tree.html b/api/jaligner/ui/images/package-tree.html
new file mode 100644
index 0000000..110c01e
--- /dev/null
+++ b/api/jaligner/ui/images/package-tree.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.images Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.images Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/logging/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.ui.images
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.ui.images.<A HREF="../../../jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images"><B>ToolbarIcons</B></A></UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/filechooser/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/logging/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/images/package-use.html b/api/jaligner/ui/images/package-use.html
new file mode 100644
index 0000000..a25559d
--- /dev/null
+++ b/api/jaligner/ui/images/package-use.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.ui.images (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.ui.images (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.ui.images</B></H2>
+</CENTER>
+No usage of jaligner.ui.images
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/DocumentHandler.html b/api/jaligner/ui/logging/DocumentHandler.html
new file mode 100644
index 0000000..d41d1dc
--- /dev/null
+++ b/api/jaligner/ui/logging/DocumentHandler.html
@@ -0,0 +1,310 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+DocumentHandler (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.logging.DocumentHandler class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="DocumentHandler (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/DocumentHandler.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="DocumentHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.logging</FONT>
+<BR>
+Class DocumentHandler</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.util.logging.Handler
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.logging.DocumentHandler</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>DocumentHandler</B><DT>extends java.util.logging.Handler</DL>
+
+<P>
+Logging handler of <CODE>JTextPane</CODE>.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/DocumentHandler.html#DocumentHandler(javax.swing.JTextPane)">DocumentHandler</A></B>(javax.swing.JTextPane textPane)</CODE>
+
+<BR>
+ Constructor</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/DocumentHandler.html#close()">close</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/DocumentHandler.html#flush()">flush</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/DocumentHandler.html#publish(java.util.logging.LogRecord)">publish</A></B>(java.util.logging.LogRecord record)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.logging.Handler"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.logging.Handler</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>getEncoding, getErrorManager, getFilter, getFormatter, getLevel, isLoggable, reportError, setEncoding, setErrorManager, setFilter, setFormatter, setLevel</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DocumentHandler(javax.swing.JTextPane)"><!-- --></A><H3>
+DocumentHandler</H3>
+<PRE>
+public <B>DocumentHandler</B>(javax.swing.JTextPane textPane)</PRE>
+<DL>
+<DD>Constructor
+<P>
+<DT><B>Parameters:</B><DD><CODE>textPane</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="close()"><!-- --></A><H3>
+close</H3>
+<PRE>
+public void <B>close</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="flush()"><!-- --></A><H3>
+flush</H3>
+<PRE>
+public void <B>flush</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="publish(java.util.logging.LogRecord)"><!-- --></A><H3>
+publish</H3>
+<PRE>
+public void <B>publish</B>(java.util.logging.LogRecord record)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/DocumentHandler.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="DocumentHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/RecordFormatter.html b/api/jaligner/ui/logging/RecordFormatter.html
new file mode 100644
index 0000000..4a1fc4e
--- /dev/null
+++ b/api/jaligner/ui/logging/RecordFormatter.html
@@ -0,0 +1,318 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+RecordFormatter (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.logging.RecordFormatter class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="RecordFormatter (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RecordFormatter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RecordFormatter.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.logging</FONT>
+<BR>
+Class RecordFormatter</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.util.logging.Formatter
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.logging.RecordFormatter</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>RecordFormatter</B><DT>extends java.util.logging.Formatter</DL>
+
+<P>
+Logging record formatter
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/RecordFormatter.html#RecordFormatter()">RecordFormatter</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/RecordFormatter.html#format(java.util.logging.LogRecord)">format</A></B>(java.util.logging.LogRecord record)</CODE>
+
+<BR>
+ This method is called for every log records</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/RecordFormatter.html#getHead(java.util.logging.Handler)">getHead</A></B>(java.util.logging.Handler handler)</CODE>
+
+<BR>
+ This method is called just after the handler using this
+ formatter is created</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/logging/RecordFormatter.html#getTail(java.util.logging.Handler)">getTail</A></B>(java.util.logging.Handler handler)</CODE>
+
+<BR>
+ This method is called just after the handler using this
+ formatter is closed</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.logging.Formatter"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.logging.Formatter</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>formatMessage</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="RecordFormatter()"><!-- --></A><H3>
+RecordFormatter</H3>
+<PRE>
+public <B>RecordFormatter</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="format(java.util.logging.LogRecord)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(java.util.logging.LogRecord record)</PRE>
+<DL>
+<DD>This method is called for every log records
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>record</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getHead(java.util.logging.Handler)"><!-- --></A><H3>
+getHead</H3>
+<PRE>
+public java.lang.String <B>getHead</B>(java.util.logging.Handler handler)</PRE>
+<DL>
+<DD>This method is called just after the handler using this
+ formatter is created
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>handler</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTail(java.util.logging.Handler)"><!-- --></A><H3>
+getTail</H3>
+<PRE>
+public java.lang.String <B>getTail</B>(java.util.logging.Handler handler)</PRE>
+<DL>
+<DD>This method is called just after the handler using this
+ formatter is closed
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>handler</CODE> - </DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RecordFormatter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RecordFormatter.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/class-use/DocumentHandler.html b/api/jaligner/ui/logging/class-use/DocumentHandler.html
new file mode 100644
index 0000000..8d264de
--- /dev/null
+++ b/api/jaligner/ui/logging/class-use/DocumentHandler.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.logging.DocumentHandler (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.logging.DocumentHandler (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="DocumentHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.logging.DocumentHandler</B></H2>
+</CENTER>
+No usage of jaligner.ui.logging.DocumentHandler
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="DocumentHandler.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/class-use/RecordFormatter.html b/api/jaligner/ui/logging/class-use/RecordFormatter.html
new file mode 100644
index 0000000..0508514
--- /dev/null
+++ b/api/jaligner/ui/logging/class-use/RecordFormatter.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.logging.RecordFormatter (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.logging.RecordFormatter (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RecordFormatter.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.logging.RecordFormatter</B></H2>
+</CENTER>
+No usage of jaligner.ui.logging.RecordFormatter
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="RecordFormatter.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/package-frame.html b/api/jaligner/ui/logging/package-frame.html
new file mode 100644
index 0000000..a2b2fd7
--- /dev/null
+++ b/api/jaligner/ui/logging/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.logging (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.logging package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../jaligner/ui/logging/package-summary.html" target="classFrame">jaligner.ui.logging</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="DocumentHandler.html" title="class in jaligner.ui.logging" target="classFrame">DocumentHandler</A>
+<BR>
+<A HREF="RecordFormatter.html" title="class in jaligner.ui.logging" target="classFrame">RecordFormatter</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/package-summary.html b/api/jaligner/ui/logging/package-summary.html
new file mode 100644
index 0000000..e7f93c4
--- /dev/null
+++ b/api/jaligner/ui/logging/package-summary.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.logging (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.logging package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.logging (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/images/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.ui.logging
+</H2>
+Logging package.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging">DocumentHandler</A></B></TD>
+<TD>Logging handler of <CODE>JTextPane</CODE>.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging">RecordFormatter</A></B></TD>
+<TD>Logging record formatter</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.ui.logging Description
+</H2>
+
+<P>
+Logging package.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/images/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/ui/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/package-tree.html b/api/jaligner/ui/logging/package-tree.html
new file mode 100644
index 0000000..7246028
--- /dev/null
+++ b/api/jaligner/ui/logging/package-tree.html
@@ -0,0 +1,149 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.logging Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.logging Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/images/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.ui.logging
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class java.util.logging.Formatter<UL>
+<LI TYPE="circle">class jaligner.ui.logging.<A HREF="../../../jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><B>RecordFormatter</B></A></UL>
+<LI TYPE="circle">class java.util.logging.Handler<UL>
+<LI TYPE="circle">class jaligner.ui.logging.<A HREF="../../../jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><B>DocumentHandler</B></A></UL>
+</UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/images/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/ui/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/logging/package-use.html b/api/jaligner/ui/logging/package-use.html
new file mode 100644
index 0000000..c0015cc
--- /dev/null
+++ b/api/jaligner/ui/logging/package-use.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.ui.logging (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.ui.logging (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
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+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.ui.logging</B></H2>
+</CENTER>
+No usage of jaligner.ui.logging
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/package-frame.html b/api/jaligner/ui/package-frame.html
new file mode 100644
index 0000000..eabccef
--- /dev/null
+++ b/api/jaligner/ui/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../jaligner/ui/package-summary.html" target="classFrame">jaligner.ui</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignCommandLine.html" title="class in jaligner.ui" target="classFrame">AlignCommandLine</A>
+<BR>
+<A HREF="AlignWindow.html" title="class in jaligner.ui" target="classFrame">AlignWindow</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/package-summary.html b/api/jaligner/ui/package-summary.html
new file mode 100644
index 0000000..321df4b
--- /dev/null
+++ b/api/jaligner/ui/package-summary.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/ui/clipboard/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.ui
+</H2>
+Command line and graphical user interface.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui">AlignCommandLine</A></B></TD>
+<TD>Command line interface for JAligner.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui">AlignWindow</A></B></TD>
+<TD>Graphical user inteface for JAligner.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.ui Description
+</H2>
+
+<P>
+Command line and graphical user interface.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../jaligner/ui/clipboard/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/package-tree.html b/api/jaligner/ui/package-tree.html
new file mode 100644
index 0000000..fe0dc17
--- /dev/null
+++ b/api/jaligner/ui/package-tree.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/ui/clipboard/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.ui
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.ui.<A HREF="../../jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><B>AlignCommandLine</B></A><LI TYPE="circle">class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.awt.Container<UL>
+<LI TYPE="circle">class java.awt.Window (implements javax.accessibility.Accessible)
+<UL>
+<LI TYPE="circle">class java.awt.Frame (implements java.awt.MenuContainer)
+<UL>
+<LI TYPE="circle">class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
+<UL>
+<LI TYPE="circle">class jaligner.ui.<A HREF="../../jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><B>AlignWindow</B></A> (implements jaligner.ui.clipboard.<A HREF="../../jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A>, javax.swing.event.DocumentListener)
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../jaligner/ui/clipboard/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/package-use.html b/api/jaligner/ui/package-use.html
new file mode 100644
index 0000000..10d448b
--- /dev/null
+++ b/api/jaligner/ui/package-use.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.ui (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.ui (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Package<br>jaligner.ui</B></H2>
+</CENTER>
+No usage of jaligner.ui
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/PrintJobMointor.html b/api/jaligner/ui/util/PrintJobMointor.html
new file mode 100644
index 0000000..aab1cce
--- /dev/null
+++ b/api/jaligner/ui/util/PrintJobMointor.html
@@ -0,0 +1,235 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+PrintJobMointor (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.util.PrintJobMointor class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="PrintJobMointor (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/PrintJobMointor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="PrintJobMointor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.util</FONT>
+<BR>
+Class PrintJobMointor</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.util.PrintJobMointor</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>PrintJobMointor</B><DT>extends java.lang.Object</DL>
+
+<P>
+Mointor for print job.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/PrintJobMointor.html#waitForPrintJob()">waitForPrintJob</A></B>()</CODE>
+
+<BR>
+ Waits for print job</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="waitForPrintJob()"><!-- --></A><H3>
+waitForPrintJob</H3>
+<PRE>
+public void <B>waitForPrintJob</B>()</PRE>
+<DL>
+<DD>Waits for print job
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/PrintJobMointor.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="PrintJobMointor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/TextComponentUtil.html b/api/jaligner/ui/util/TextComponentUtil.html
new file mode 100644
index 0000000..153b40c
--- /dev/null
+++ b/api/jaligner/ui/util/TextComponentUtil.html
@@ -0,0 +1,449 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+TextComponentUtil (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.util.TextComponentUtil class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="TextComponentUtil (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/TextComponentUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtil.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.util</FONT>
+<BR>
+Class TextComponentUtil</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.util.TextComponentUtil</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>TextComponentUtil</B><DT>extends java.lang.Object</DL>
+
+<P>
+Text component (e.g. <CODE>JTextArea</CODE>or
+ <CODE>JTextPane</CODE>) editing helper class.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#TextComponentUtil()">TextComponentUtil</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#copy(javax.swing.text.JTextComponent)">copy</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Copies the selected text to the system clipboard.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#cut(javax.swing.text.JTextComponent)">cut</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Copies the selected text to the system clipboad and then deletes it from
+ the text component.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#delete(javax.swing.text.JTextComponent)">delete</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Deletes the selected text in a text component.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#open(javax.swing.text.JTextComponent)">open</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Opens a file and puts the contents of the file in a text component.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#paste(javax.swing.text.JTextComponent)">paste</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Copies the text contents of the system clipboard to the text component.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#print(javax.swing.text.JTextComponent)">print</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Prints the contents of a text component.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#save(javax.swing.text.JTextComponent)">save</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Saves the contents of a text component to a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#save(javax.swing.text.JTextComponent, java.lang.String)">save</A></B>(javax.swing.text.JTextComponent textComponent,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves the contents of a text component to a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html#selectAll(javax.swing.text.JTextComponent)">selectAll</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Selects all contents of a text component.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="TextComponentUtil()"><!-- --></A><H3>
+TextComponentUtil</H3>
+<PRE>
+public <B>TextComponentUtil</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="cut(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+cut</H3>
+<PRE>
+public static void <B>cut</B>(javax.swing.text.JTextComponent textComponent)</PRE>
+<DL>
+<DD>Copies the selected text to the system clipboad and then deletes it from
+ the text component.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="copy(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+copy</H3>
+<PRE>
+public static void <B>copy</B>(javax.swing.text.JTextComponent textComponent)</PRE>
+<DL>
+<DD>Copies the selected text to the system clipboard.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paste(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+paste</H3>
+<PRE>
+public static void <B>paste</B>(javax.swing.text.JTextComponent textComponent)</PRE>
+<DL>
+<DD>Copies the text contents of the system clipboard to the text component.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="delete(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+delete</H3>
+<PRE>
+public static void <B>delete</B>(javax.swing.text.JTextComponent textComponent)</PRE>
+<DL>
+<DD>Deletes the selected text in a text component.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="selectAll(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+selectAll</H3>
+<PRE>
+public static void <B>selectAll</B>(javax.swing.text.JTextComponent textComponent)</PRE>
+<DL>
+<DD>Selects all contents of a text component.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="open(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+open</H3>
+<PRE>
+public static boolean <B>open</B>(javax.swing.text.JTextComponent textComponent)
+ throws <A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></PRE>
+<DL>
+<DD>Opens a file and puts the contents of the file in a text component.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> -
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="save(javax.swing.text.JTextComponent, java.lang.String)"><!-- --></A><H3>
+save</H3>
+<PRE>
+public static boolean <B>save</B>(javax.swing.text.JTextComponent textComponent,
+ java.lang.String fileName)
+ throws <A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></PRE>
+<DL>
+<DD>Saves the contents of a text component to a file.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> - <DD><CODE>fileName</CODE> -
+<DT><B>Returns:</B><DD>true if a file has been chosen or false otherwise
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="save(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+save</H3>
+<PRE>
+public static boolean <B>save</B>(javax.swing.text.JTextComponent textComponent)
+ throws <A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></PRE>
+<DL>
+<DD>Saves the contents of a text component to a file.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> -
+<DT><B>Returns:</B><DD>true if a file has been chosen or false otherwise
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="print(javax.swing.text.JTextComponent)"><!-- --></A><H3>
+print</H3>
+<PRE>
+public static void <B>print</B>(javax.swing.text.JTextComponent textComponent)
+ throws <A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></PRE>
+<DL>
+<DD>Prints the contents of a text component.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>textComponent</CODE> -
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/TextComponentUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtil.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/TextComponentUtilException.html b/api/jaligner/ui/util/TextComponentUtilException.html
new file mode 100644
index 0000000..cb8ca67
--- /dev/null
+++ b/api/jaligner/ui/util/TextComponentUtilException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+TextComponentUtilException (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.util.TextComponentUtilException class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="TextComponentUtilException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/TextComponentUtilException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtilException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.ui.util</FONT>
+<BR>
+Class TextComponentUtilException</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.lang.Throwable
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by">java.lang.Exception
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by"><B>jaligner.ui.util.TextComponentUtilException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>TextComponentUtilException</B><DT>extends java.lang.Exception</DL>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../serialized-form.html#jaligner.ui.util.TextComponentUtilException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../jaligner/ui/util/TextComponentUtilException.html#TextComponentUtilException(java.lang.String)">TextComponentUtilException</A></B>(java.lang.String message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Throwable</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="TextComponentUtilException(java.lang.String)"><!-- --></A><H3>
+TextComponentUtilException</H3>
+<PRE>
+public <B>TextComponentUtilException</B>(java.lang.String message)</PRE>
+<DL>
+<DT><B>Parameters:</B><DD><CODE>message</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/TextComponentUtilException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtilException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/class-use/PrintJobMointor.html b/api/jaligner/ui/util/class-use/PrintJobMointor.html
new file mode 100644
index 0000000..4cff19c
--- /dev/null
+++ b/api/jaligner/ui/util/class-use/PrintJobMointor.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.util.PrintJobMointor (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.util.PrintJobMointor (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="PrintJobMointor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.util.PrintJobMointor</B></H2>
+</CENTER>
+No usage of jaligner.ui.util.PrintJobMointor
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="PrintJobMointor.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/class-use/TextComponentUtil.html b/api/jaligner/ui/util/class-use/TextComponentUtil.html
new file mode 100644
index 0000000..093e4b1
--- /dev/null
+++ b/api/jaligner/ui/util/class-use/TextComponentUtil.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.util.TextComponentUtil (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.util.TextComponentUtil (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtil.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.util.TextComponentUtil</B></H2>
+</CENTER>
+No usage of jaligner.ui.util.TextComponentUtil
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtil.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/class-use/TextComponentUtilException.html b/api/jaligner/ui/util/class-use/TextComponentUtilException.html
new file mode 100644
index 0000000..678e3b6
--- /dev/null
+++ b/api/jaligner/ui/util/class-use/TextComponentUtilException.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.ui.util.TextComponentUtilException (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.ui.util.TextComponentUtilException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtilException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.ui.util.TextComponentUtilException</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.util"><B>jaligner.ui.util</B></A></TD>
+<TD>Text component utilites package. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.util"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A> in <A HREF="../../../../jaligner/ui/util/package-summary.html">jaligner.ui.util</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../../jaligner/ui/util/package-summary.html">jaligner.ui.util</A> that throw <A HREF="../../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B>TextComponentUtil.</B><B><A HREF="../../../../jaligner/ui/util/TextComponentUtil.html#open(javax.swing.text.JTextComponent)">open</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Opens a file and puts the contents of the file in a text component.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B>TextComponentUtil.</B><B><A HREF="../../../../jaligner/ui/util/TextComponentUtil.html#save(javax.swing.text.JTextComponent, java.lang.String)">save</A></B>(javax.swing.text.JTextComponent textComponent,
+ java.lang.String fileName)</CODE>
+
+<BR>
+ Saves the contents of a text component to a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B>TextComponentUtil.</B><B><A HREF="../../../../jaligner/ui/util/TextComponentUtil.html#save(javax.swing.text.JTextComponent)">save</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Saves the contents of a text component to a file.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B>TextComponentUtil.</B><B><A HREF="../../../../jaligner/ui/util/TextComponentUtil.html#print(javax.swing.text.JTextComponent)">print</A></B>(javax.swing.text.JTextComponent textComponent)</CODE>
+
+<BR>
+ Prints the contents of a text component.</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="TextComponentUtilException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/package-frame.html b/api/jaligner/ui/util/package-frame.html
new file mode 100644
index 0000000..6117b5a
--- /dev/null
+++ b/api/jaligner/ui/util/package-frame.html
@@ -0,0 +1,45 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.util (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.util package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../jaligner/ui/util/package-summary.html" target="classFrame">jaligner.ui.util</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="PrintJobMointor.html" title="class in jaligner.ui.util" target="classFrame">PrintJobMointor</A>
+<BR>
+<A HREF="TextComponentUtil.html" title="class in jaligner.ui.util" target="classFrame">TextComponentUtil</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="TextComponentUtilException.html" title="class in jaligner.ui.util" target="classFrame">TextComponentUtilException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/package-summary.html b/api/jaligner/ui/util/package-summary.html
new file mode 100644
index 0000000..e61a820
--- /dev/null
+++ b/api/jaligner/ui/util/package-summary.html
@@ -0,0 +1,185 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.util (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.ui.util package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
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+{
+ parent.document.title="jaligner.ui.util (JAligner)";
+}
+</SCRIPT>
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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+ </TR>
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/logging/package-summary.html"><B>PREV PACKAGE</B></A>
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+<H2>
+Package jaligner.ui.util
+</H2>
+Text component utilites package.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util">PrintJobMointor</A></B></TD>
+<TD>Mointor for print job.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util">TextComponentUtil</A></B></TD>
+<TD>Text component (e.g.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">TextComponentUtilException</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.ui.util Description
+</H2>
+
+<P>
+Text component utilites package.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/logging/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../jaligner/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <!--
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+ //-->
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+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/package-tree.html b/api/jaligner/ui/util/package-tree.html
new file mode 100644
index 0000000..4ed66c5
--- /dev/null
+++ b/api/jaligner/ui/util/package-tree.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.ui.util Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.ui.util Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
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+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/logging/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
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+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.ui.util
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.ui.util.<A HREF="../../../jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><B>PrintJobMointor</B></A><LI TYPE="circle">class jaligner.ui.util.<A HREF="../../../jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><B>TextComponentUtil</B></A><LI TYPE="circle">class java.lang.Throwable (implements java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.lang.Exception<UL>
+<LI TYPE="circle">class jaligner.ui.util.<A HREF="../../../jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util"><B>TextComponentUtilException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../jaligner/ui/logging/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../jaligner/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ //-->
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+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/ui/util/package-use.html b/api/jaligner/ui/util/package-use.html
new file mode 100644
index 0000000..2766152
--- /dev/null
+++ b/api/jaligner/ui/util/package-use.html
@@ -0,0 +1,162 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.ui.util (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.ui.util (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
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+<H2>
+<B>Uses of Package<br>jaligner.ui.util</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/ui/util/package-summary.html">jaligner.ui.util</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.ui.util"><B>jaligner.ui.util</B></A></TD>
+<TD>Text component utilites package. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.util"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../../jaligner/ui/util/package-summary.html">jaligner.ui.util</A> used by <A HREF="../../../jaligner/ui/util/package-summary.html">jaligner.ui.util</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../../jaligner/ui/util/class-use/TextComponentUtilException.html#jaligner.ui.util"><B>TextComponentUtilException</B></A></B>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/Commons.html b/api/jaligner/util/Commons.html
new file mode 100644
index 0000000..7562fc1
--- /dev/null
+++ b/api/jaligner/util/Commons.html
@@ -0,0 +1,394 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Commons (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.util.Commons class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Commons (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Commons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/util/SequenceParser.html" title="class in jaligner.util"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Commons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.util</FONT>
+<BR>
+Class Commons</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.util.Commons</B>
+</PRE>
+<HR>
+<DL>
+<DT>public abstract class <B>Commons</B><DT>extends java.lang.Object</DL>
+
+<P>
+Global constants/varilables/settings
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#Commons()">Commons</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#getCurrentRelease()">getCurrentRelease</A></B>()</CODE>
+
+<BR>
+ Returns the current release version of JAligner</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#getFileSeparator()">getFileSeparator</A></B>()</CODE>
+
+<BR>
+ Returns system file separator.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#getJAlignerInfo()">getJAlignerInfo</A></B>()</CODE>
+
+<BR>
+ Returns information about JAligner</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#getLineSeparator()">getLineSeparator</A></B>()</CODE>
+
+<BR>
+ Returns system line separator.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#getUserDirectory()">getUserDirectory</A></B>()</CODE>
+
+<BR>
+ Returns user's current directory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#isJnlp()">isJnlp</A></B>()</CODE>
+
+<BR>
+ Returns true if jnlp is enabled</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#setJnlp(boolean)">setJnlp</A></B>(boolean jnlp)</CODE>
+
+<BR>
+ Sets the JNLP flag to true of false</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Commons()"><!-- --></A><H3>
+Commons</H3>
+<PRE>
+public <B>Commons</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFileSeparator()"><!-- --></A><H3>
+getFileSeparator</H3>
+<PRE>
+public static java.lang.String <B>getFileSeparator</B>()</PRE>
+<DL>
+<DD>Returns system file separator.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>file separator</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLineSeparator()"><!-- --></A><H3>
+getLineSeparator</H3>
+<PRE>
+public static java.lang.String <B>getLineSeparator</B>()</PRE>
+<DL>
+<DD>Returns system line separator.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>line separator</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUserDirectory()"><!-- --></A><H3>
+getUserDirectory</H3>
+<PRE>
+public static java.lang.String <B>getUserDirectory</B>()</PRE>
+<DL>
+<DD>Returns user's current directory.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>user's current directory</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setJnlp(boolean)"><!-- --></A><H3>
+setJnlp</H3>
+<PRE>
+public static void <B>setJnlp</B>(boolean jnlp)</PRE>
+<DL>
+<DD>Sets the JNLP flag to true of false
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>jnlp</CODE> - true or false</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isJnlp()"><!-- --></A><H3>
+isJnlp</H3>
+<PRE>
+public static boolean <B>isJnlp</B>()</PRE>
+<DL>
+<DD>Returns true if jnlp is enabled
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>true if jnlp is enabled, otherwise returns false</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentRelease()"><!-- --></A><H3>
+getCurrentRelease</H3>
+<PRE>
+public static java.lang.String <B>getCurrentRelease</B>()</PRE>
+<DL>
+<DD>Returns the current release version of JAligner
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>current release</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getJAlignerInfo()"><!-- --></A><H3>
+getJAlignerInfo</H3>
+<PRE>
+public static java.lang.String <B>getJAlignerInfo</B>()</PRE>
+<DL>
+<DD>Returns information about JAligner
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>information about JAligner</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Commons.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../jaligner/util/SequenceParser.html" title="class in jaligner.util"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Commons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/SequenceParser.html b/api/jaligner/util/SequenceParser.html
new file mode 100644
index 0000000..e164e71
--- /dev/null
+++ b/api/jaligner/util/SequenceParser.html
@@ -0,0 +1,297 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+SequenceParser (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.util.SequenceParser class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="SequenceParser (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SequenceParser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/util/Commons.html" title="class in jaligner.util"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceParser.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.util</FONT>
+<BR>
+Class SequenceParser</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.util.SequenceParser</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceParser</B><DT>extends java.lang.Object</DL>
+
+<P>
+SequenceParser to sequences from different formats.
+ <br>
+ Currently the supported formats are:
+ <ul>
+ <li>Plain sequence</li>
+ <li><a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">Sequence</a></li>
+ </ul>
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/util/SequenceParser.html#SequenceParser()">SequenceParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/SequenceParser.html#parse(java.io.File)">parse</A></B>(java.io.File file)</CODE>
+
+<BR>
+ Returns a Sequence parsed and loaded from a file</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../jaligner/util/SequenceParser.html#parse(java.lang.String)">parse</A></B>(java.lang.String sequence)</CODE>
+
+<BR>
+ Returns a parsed Sequence from a string.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceParser()"><!-- --></A><H3>
+SequenceParser</H3>
+<PRE>
+public <B>SequenceParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="parse(java.lang.String)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public static <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> <B>parse</B>(java.lang.String sequence)
+ throws <A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></PRE>
+<DL>
+<DD>Returns a parsed Sequence from a string.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - string to parse
+<DT><B>Returns:</B><DD>parsed sequence
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../jaligner/Sequence.html" title="class in jaligner"><CODE>Sequence</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="parse(java.io.File)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public static <A HREF="../../jaligner/Sequence.html" title="class in jaligner">Sequence</A> <B>parse</B>(java.io.File file)
+ throws <A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></PRE>
+<DL>
+<DD>Returns a Sequence parsed and loaded from a file
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>file</CODE> - to parse
+<DT><B>Returns:</B><DD>parsed sequence
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></CODE><DT><B>See Also:</B><DD><A HREF="../../jaligner/Sequence.html" title="class in jaligner"><CODE>Sequence</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SequenceParser.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/util/Commons.html" title="class in jaligner.util"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceParser.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/SequenceParserException.html b/api/jaligner/util/SequenceParserException.html
new file mode 100644
index 0000000..38f7b59
--- /dev/null
+++ b/api/jaligner/util/SequenceParserException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+SequenceParserException (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.util.SequenceParserException class">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="SequenceParserException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SequenceParserException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceParserException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+jaligner.util</FONT>
+<BR>
+Class SequenceParserException</H2>
+<PRE>
+java.lang.Object
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.lang.Throwable
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by">java.lang.Exception
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by"><B>jaligner.util.SequenceParserException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceParserException</B><DT>extends java.lang.Exception</DL>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#jaligner.util.SequenceParserException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../jaligner/util/SequenceParserException.html#SequenceParserException(java.lang.String)">SequenceParserException</A></B>(java.lang.String message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Throwable</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString</CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.Object</B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceParserException(java.lang.String)"><!-- --></A><H3>
+SequenceParserException</H3>
+<PRE>
+public <B>SequenceParserException</B>(java.lang.String message)</PRE>
+<DL>
+<DT><B>Parameters:</B><DD><CODE>message</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SequenceParserException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceParserException.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/class-use/Commons.html b/api/jaligner/util/class-use/Commons.html
new file mode 100644
index 0000000..d6747f9
--- /dev/null
+++ b/api/jaligner/util/class-use/Commons.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.util.Commons (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.util.Commons (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/util/Commons.html" title="class in jaligner.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="Commons.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.util.Commons</B></H2>
+</CENTER>
+No usage of jaligner.util.Commons
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/class-use/SequenceParser.html b/api/jaligner/util/class-use/SequenceParser.html
new file mode 100644
index 0000000..78fb9d8
--- /dev/null
+++ b/api/jaligner/util/class-use/SequenceParser.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.util.SequenceParser (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.util.SequenceParser (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
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+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/util/SequenceParser.html" title="class in jaligner.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.util.SequenceParser</B></H2>
+</CENTER>
+No usage of jaligner.util.SequenceParser
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/util/SequenceParser.html" title="class in jaligner.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
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+ PREV
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
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+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/class-use/SequenceParserException.html b/api/jaligner/util/class-use/SequenceParserException.html
new file mode 100644
index 0000000..88c30d5
--- /dev/null
+++ b/api/jaligner/util/class-use/SequenceParserException.html
@@ -0,0 +1,180 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Class jaligner.util.SequenceParserException (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Class jaligner.util.SequenceParserException (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
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+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/util/SequenceParserException.html" title="class in jaligner.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
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+<HR>
+<CENTER>
+<H2>
+<B>Uses of Class<br>jaligner.util.SequenceParserException</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.util"><B>jaligner.util</B></A></TD>
+<TD>Utility classes for helping core and GUI classes. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.util"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Uses of <A HREF="../../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A> in <A HREF="../../../jaligner/util/package-summary.html">jaligner.util</A></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2>Methods in <A HREF="../../../jaligner/util/package-summary.html">jaligner.util</A> that throw <A HREF="../../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B>SequenceParser.</B><B><A HREF="../../../jaligner/util/SequenceParser.html#parse(java.lang.String)">parse</A></B>(java.lang.String sequence)</CODE>
+
+<BR>
+ Returns a parsed Sequence from a string.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B>SequenceParser.</B><B><A HREF="../../../jaligner/util/SequenceParser.html#parse(java.io.File)">parse</A></B>(java.io.File file)</CODE>
+
+<BR>
+ Returns a Sequence parsed and loaded from a file</TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../jaligner/util/SequenceParserException.html" title="class in jaligner.util"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ //-->
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+<NOSCRIPT>
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/package-frame.html b/api/jaligner/util/package-frame.html
new file mode 100644
index 0000000..553274c
--- /dev/null
+++ b/api/jaligner/util/package-frame.html
@@ -0,0 +1,45 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.util (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.util package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../jaligner/util/package-summary.html" target="classFrame">jaligner.util</A></FONT>
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Commons.html" title="class in jaligner.util" target="classFrame">Commons</A>
+<BR>
+<A HREF="SequenceParser.html" title="class in jaligner.util" target="classFrame">SequenceParser</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceParserException.html" title="class in jaligner.util" target="classFrame">SequenceParserException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/package-summary.html b/api/jaligner/util/package-summary.html
new file mode 100644
index 0000000..5f5b492
--- /dev/null
+++ b/api/jaligner/util/package-summary.html
@@ -0,0 +1,185 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.util (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="jaligner.util package">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.util (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/ui/util/package-summary.html"><B>PREV PACKAGE</B></A>
+ NEXT PACKAGE</FONT></TD>
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+ <!--
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+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<H2>
+Package jaligner.util
+</H2>
+Utility classes for helping core and GUI classes.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/util/Commons.html" title="class in jaligner.util">Commons</A></B></TD>
+<TD>Global constants/varilables/settings</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/util/SequenceParser.html" title="class in jaligner.util">SequenceParser</A></B></TD>
+<TD>SequenceParser to sequences from different formats.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package jaligner.util Description
+</H2>
+
+<P>
+Utility classes for helping core and GUI classes.
+<P>
+
+<P>
+<DL>
+<DT><B>Author:</B></DT>
+ <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
+</DL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/ui/util/package-summary.html"><B>PREV PACKAGE</B></A>
+ NEXT PACKAGE</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <!--
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+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/package-tree.html b/api/jaligner/util/package-tree.html
new file mode 100644
index 0000000..af6714b
--- /dev/null
+++ b/api/jaligner/util/package-tree.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+jaligner.util Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="jaligner.util Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/ui/util/package-tree.html"><B>PREV</B></A>
+ NEXT</FONT></TD>
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+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package jaligner.util
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.util.<A HREF="../../jaligner/util/Commons.html" title="class in jaligner.util"><B>Commons</B></A><LI TYPE="circle">class jaligner.util.<A HREF="../../jaligner/util/SequenceParser.html" title="class in jaligner.util"><B>SequenceParser</B></A><LI TYPE="circle">class java.lang.Throwable (implements java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.lang.Exception<UL>
+<LI TYPE="circle">class jaligner.util.<A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util"><B>SequenceParserException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../jaligner/ui/util/package-tree.html"><B>PREV</B></A>
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
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+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
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+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/jaligner/util/package-use.html b/api/jaligner/util/package-use.html
new file mode 100644
index 0000000..9a26eaf
--- /dev/null
+++ b/api/jaligner/util/package-use.html
@@ -0,0 +1,162 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Uses of Package jaligner.util (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Uses of Package jaligner.util (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+<H2>
+<B>Uses of Package<br>jaligner.util</B></H2>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Packages that use <A HREF="../../jaligner/util/package-summary.html">jaligner.util</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#jaligner.util"><B>jaligner.util</B></A></TD>
+<TD>Utility classes for helping core and GUI classes. </TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.util"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+Classes in <A HREF="../../jaligner/util/package-summary.html">jaligner.util</A> used by <A HREF="../../jaligner/util/package-summary.html">jaligner.util</A></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><B><A HREF="../../jaligner/util/class-use/SequenceParserException.html#jaligner.util"><B>SequenceParserException</B></A></B>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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+ <!--
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+ //-->
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+<NOSCRIPT>
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/overview-frame.html b/api/overview-frame.html
new file mode 100644
index 0000000..2546a12
--- /dev/null
+++ b/api/overview-frame.html
@@ -0,0 +1,64 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Overview (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="Overview, JAligner: Java implementation of Smith-Waterman algorithm for sequence alignment">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameTitleFont">
+<B><a href="http://jaligner.sourceforge.net">JAligner</a></B></FONT></TD>
+</TR>
+</TABLE>
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="allclasses-frame.html" target="packageFrame">All Classes</A></FONT>
+<P>
+<FONT size="+1" CLASS="FrameHeadingFont">
+Packages</FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/package-frame.html" target="packageFrame">jaligner</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/example/package-frame.html" target="packageFrame">jaligner.example</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/formats/package-frame.html" target="packageFrame">jaligner.formats</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/matrix/package-frame.html" target="packageFrame">jaligner.matrix</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/test/package-frame.html" target="packageFrame">jaligner.test</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/package-frame.html" target="packageFrame">jaligner.ui</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/clipboard/package-frame.html" target="packageFrame">jaligner.ui.clipboard</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/filechooser/package-frame.html" target="packageFrame">jaligner.ui.filechooser</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/images/package-frame.html" target="packageFrame">jaligner.ui.images</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/logging/package-frame.html" target="packageFrame">jaligner.ui.logging</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/ui/util/package-frame.html" target="packageFrame">jaligner.ui.util</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="jaligner/util/package-frame.html" target="packageFrame">jaligner.util</A></FONT>
+<BR>
+</TD>
+</TR>
+</TABLE>
+
+<P>
+
+</BODY>
+</HTML>
diff --git a/api/overview-summary.html b/api/overview-summary.html
new file mode 100644
index 0000000..ffcb89b
--- /dev/null
+++ b/api/overview-summary.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Overview (JAligner)
+</TITLE>
+
+<META NAME="keywords" CONTENT="Overview, JAligner: Java implementation of Smith-Waterman algorithm for sequence alignment">
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Overview (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="overview-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H1>
+JAligner: Java implementation of Smith-Waterman algorithm for sequence alignment
+</H1>
+</CENTER>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Packages</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/package-summary.html">jaligner</A></B></TD>
+<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/example/package-summary.html">jaligner.example</A></B></TD>
+<TD>Example for using API of JAligner to perform pairwise sequence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/formats/package-summary.html">jaligner.formats</A></B></TD>
+<TD>Group of formats for output alignments.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/matrix/package-summary.html">jaligner.matrix</A></B></TD>
+<TD>Scoring matrices package.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/test/package-summary.html">jaligner.test</A></B></TD>
+<TD>Testing package.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/ui/package-summary.html">jaligner.ui</A></B></TD>
+<TD>Command line and graphical user interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/ui/clipboard/package-summary.html">jaligner.ui.clipboard</A></B></TD>
+<TD>Clipboard handling for JNLP and AWT.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/ui/filechooser/package-summary.html">jaligner.ui.filechooser</A></B></TD>
+<TD>File loading and storing.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/ui/images/package-summary.html">jaligner.ui.images</A></B></TD>
+<TD>Images used in the toolbar.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/ui/logging/package-summary.html">jaligner.ui.logging</A></B></TD>
+<TD>Logging package.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/ui/util/package-summary.html">jaligner.ui.util</A></B></TD>
+<TD>Text component utilites package.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="jaligner/util/package-summary.html">jaligner.util</A></B></TD>
+<TD>Utility classes for helping core and GUI classes.</TD>
+</TR>
+</TABLE>
+
+<P>
+ <HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="overview-summary.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/overview-tree.html b/api/overview-tree.html
new file mode 100644
index 0000000..9a68d44
--- /dev/null
+++ b/api/overview-tree.html
@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+Class Hierarchy (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Class Hierarchy (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="overview-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For All Packages</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="jaligner/package-tree.html">jaligner</A>, <A HREF="jaligner/example/package-tree.html">jaligner.example</A>, <A HREF="jaligner/formats/package-tree.html">jaligner.formats</A>, <A HREF="jaligner/matrix/package-tree.html">jaligner.matrix</A>, <A HREF="jaligner/test/package-tree.html">jaligner.test</A>, <A HREF="jaligner/ui/package-tree.html">jaligner.ui</A>, <A HREF="jaligner/ui/clipboard/package-tree.html">jaligner.ui.clipboard</A>, <A HREF="jal [...]
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class jaligner.ui.<A HREF="jaligner/ui/AlignCommandLine.html" title="class in jaligner.ui"><B>AlignCommandLine</B></A><LI TYPE="circle">class jaligner.<A HREF="jaligner/Alignment.html" title="class in jaligner"><B>Alignment</B></A><LI TYPE="circle">class jaligner.test.<A HREF="jaligner/test/AlignmentScoreChecker.html" title="class in jaligner.test"><B>AlignmentScoreChecker</B></A><LI TYPE="circle">class jaligner.<A HREF="jaligner/Cell.html" title="class in jaligner"><B> [...]
+<LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerFactory</B></A><LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandlerJNLP.html" title="class in jaligner.ui.clipboard"><B>ClipboardHandlerJNLP</B></A> (implements jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard">Clipbo [...]
+<LI TYPE="circle">class jaligner.util.<A HREF="jaligner/util/Commons.html" title="class in jaligner.util"><B>Commons</B></A><LI TYPE="circle">class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.awt.Container<UL>
+<LI TYPE="circle">class java.awt.Window (implements javax.accessibility.Accessible)
+<UL>
+<LI TYPE="circle">class java.awt.Frame (implements java.awt.MenuContainer)
+<UL>
+<LI TYPE="circle">class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
+<UL>
+<LI TYPE="circle">class jaligner.ui.<A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui"><B>AlignWindow</B></A> (implements jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard">ClipboardListener</A>, javax.swing.event.DocumentListener)
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class jaligner.<A HREF="jaligner/Directions.html" title="class in jaligner"><B>Directions</B></A><LI TYPE="circle">class jaligner.example.<A HREF="jaligner/example/Example.html" title="class in jaligner.example"><B>Example</B></A><LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooser.html" title="class in jaligner.ui.filechooser"><B>FileChooser</B></A><UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserJNLP.html" title="class in jaligner.ui.filechooser"><B>FileChooserJNLP</B></A><LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserTrusted.html" title="class in jaligner.ui.filechooser"><B>FileChooserTrusted</B></A></UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserFactory.html" title="class in jaligner.ui.filechooser"><B>FileChooserFactory</B></A><LI TYPE="circle">class jaligner.formats.<A HREF="jaligner/formats/Format.html" title="class in jaligner.formats"><B>Format</B></A><UL>
+<LI TYPE="circle">class jaligner.formats.<A HREF="jaligner/formats/CLUSTAL.html" title="class in jaligner.formats"><B>CLUSTAL</B></A><LI TYPE="circle">class jaligner.formats.<A HREF="jaligner/formats/FASTA.html" title="class in jaligner.formats"><B>FASTA</B></A><LI TYPE="circle">class jaligner.formats.<A HREF="jaligner/formats/Pair.html" title="class in jaligner.formats"><B>Pair</B></A></UL>
+<LI TYPE="circle">class jaligner.formats.<A HREF="jaligner/formats/FormatFactory.html" title="class in jaligner.formats"><B>FormatFactory</B></A><LI TYPE="circle">class java.util.logging.Formatter<UL>
+<LI TYPE="circle">class jaligner.ui.logging.<A HREF="jaligner/ui/logging/RecordFormatter.html" title="class in jaligner.ui.logging"><B>RecordFormatter</B></A></UL>
+<LI TYPE="circle">class java.util.logging.Handler<UL>
+<LI TYPE="circle">class jaligner.ui.logging.<A HREF="jaligner/ui/logging/DocumentHandler.html" title="class in jaligner.ui.logging"><B>DocumentHandler</B></A></UL>
+<LI TYPE="circle">class jaligner.<A HREF="jaligner/Markups.html" title="class in jaligner"><B>Markups</B></A><LI TYPE="circle">class jaligner.matrix.<A HREF="jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><B>MatricesCompartor</B></A> (implements java.util.Comparator)
+<LI TYPE="circle">class jaligner.matrix.<A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix"><B>Matrix</B></A> (implements java.io.Serializable)
+<LI TYPE="circle">class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoader.html" title="class in jaligner.matrix"><B>MatrixLoader</B></A><LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser"><B>NamedInputStream</B></A> (implements java.io.Serializable)
+<LI TYPE="circle">class jaligner.ui.util.<A HREF="jaligner/ui/util/PrintJobMointor.html" title="class in jaligner.ui.util"><B>PrintJobMointor</B></A><LI TYPE="circle">class jaligner.test.<A HREF="jaligner/test/RandomSequenceGenerator.html" title="class in jaligner.test"><B>RandomSequenceGenerator</B></A><LI TYPE="circle">class jaligner.<A HREF="jaligner/Sequence.html" title="class in jaligner"><B>Sequence</B></A> (implements java.io.Serializable)
+<LI TYPE="circle">class jaligner.util.<A HREF="jaligner/util/SequenceParser.html" title="class in jaligner.util"><B>SequenceParser</B></A><LI TYPE="circle">class jaligner.<A HREF="jaligner/SmithWatermanGotoh.html" title="class in jaligner"><B>SmithWatermanGotoh</B></A><LI TYPE="circle">class jaligner.ui.util.<A HREF="jaligner/ui/util/TextComponentUtil.html" title="class in jaligner.ui.util"><B>TextComponentUtil</B></A><LI TYPE="circle">class java.lang.Thread (implements java.lang.Runnable)
+<UL>
+<LI TYPE="circle">class jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard"><B>ClipboardPoller</B></A></UL>
+<LI TYPE="circle">class java.lang.Throwable (implements java.io.Serializable)
+<UL>
+<LI TYPE="circle">class java.lang.Exception<UL>
+<LI TYPE="circle">class jaligner.ui.filechooser.<A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser"><B>FileChooserException</B></A><LI TYPE="circle">class jaligner.matrix.<A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix"><B>MatrixLoaderException</B></A><LI TYPE="circle">class jaligner.util.<A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util"><B>SequenceParserException</B></ [...]
+</UL>
+<LI TYPE="circle">class jaligner.ui.images.<A HREF="jaligner/ui/images/ToolbarIcons.html" title="class in jaligner.ui.images"><B>ToolbarIcons</B></A></UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardHandler.html" title="interface in jaligner.ui.clipboard"><B>ClipboardHandler</B></A><LI TYPE="circle">interface jaligner.ui.clipboard.<A HREF="jaligner/ui/clipboard/ClipboardListener.html" title="interface in jaligner.ui.clipboard"><B>ClipboardListener</B></A></UL>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="overview-tree.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/api/package-list b/api/package-list
new file mode 100644
index 0000000..34b4a0c
--- /dev/null
+++ b/api/package-list
@@ -0,0 +1,12 @@
+jaligner
+jaligner.example
+jaligner.formats
+jaligner.matrix
+jaligner.test
+jaligner.ui
+jaligner.ui.clipboard
+jaligner.ui.filechooser
+jaligner.ui.images
+jaligner.ui.logging
+jaligner.ui.util
+jaligner.util
diff --git a/api/packages.html b/api/packages.html
new file mode 100644
index 0000000..1c6efb7
--- /dev/null
+++ b/api/packages.html
@@ -0,0 +1,37 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
+<TITLE>
+ (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title=" (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+<BR>
+
+<BR>
+
+<BR>
+<CENTER>
+The front page has been relocated.Please see:
+<BR>
+ <A HREF="index.html">Frame version</A>
+<BR>
+ <A HREF="overview-summary.html">Non-frame version.</A></CENTER>
+
+</BODY>
+</HTML>
diff --git a/api/resources/inherit.gif b/api/resources/inherit.gif
new file mode 100644
index 0000000..c814867
Binary files /dev/null and b/api/resources/inherit.gif differ
diff --git a/api/serialized-form.html b/api/serialized-form.html
new file mode 100644
index 0000000..6d1fa02
--- /dev/null
+++ b/api/serialized-form.html
@@ -0,0 +1,1232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:24 PDT 2005 -->
+<TITLE>
+Serialized Form (JAligner)
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="jaligner.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Serialized Form (JAligner)";
+}
+</SCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="serialized-form.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H1>
+Serialized Form</H1>
+</CENTER>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>jaligner</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.Sequence"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/Sequence.html" title="class in jaligner">jaligner.Sequence</A> extends java.lang.Object implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3256721801357898297l
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+sequence</H3>
+<PRE>
+java.lang.String <B>sequence</B></PRE>
+<DL>
+<DD>Sequence
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+id</H3>
+<PRE>
+java.lang.String <B>id</B></PRE>
+<DL>
+<DD>Sequence id.
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+description</H3>
+<PRE>
+java.lang.String <B>description</B></PRE>
+<DL>
+<DD>Sequence description.
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+type</H3>
+<PRE>
+int <B>type</B></PRE>
+<DL>
+<DD>Sequence type.
+<P>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>jaligner.matrix</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.matrix.Matrix"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/matrix/Matrix.html" title="class in jaligner.matrix">jaligner.matrix.Matrix</A> extends java.lang.Object implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3833742170619524400l
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+id</H3>
+<PRE>
+java.lang.String <B>id</B></PRE>
+<DL>
+<DD>Matrix id (or name)
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+scores</H3>
+<PRE>
+float[][] <B>scores</B></PRE>
+<DL>
+<DD>Scores
+<P>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="jaligner.matrix.MatrixLoaderException"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/matrix/MatrixLoaderException.html" title="class in jaligner.matrix">jaligner.matrix.MatrixLoaderException</A> extends java.lang.Exception implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3906364935142586680l
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>jaligner.ui</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.AlignWindow"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/ui/AlignWindow.html" title="class in jaligner.ui">jaligner.ui.AlignWindow</A> extends javax.swing.JFrame implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3257844376876364850l
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+clipboardPoller</H3>
+<PRE>
+<A HREF="jaligner/ui/clipboard/ClipboardPoller.html" title="class in jaligner.ui.clipboard">ClipboardPoller</A> <B>clipboardPoller</B></PRE>
+<DL>
+<DD>Clipboard poller thread
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+matrices</H3>
+<PRE>
+java.util.HashMap <B>matrices</B></PRE>
+<DL>
+<DD>Loaded scoring matrices
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+currentTextComponent</H3>
+<PRE>
+javax.swing.text.JTextComponent <B>currentTextComponent</B></PRE>
+<DL>
+<DD>Current text component
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+nextFocusAction</H3>
+<PRE>
+javax.swing.Action <B>nextFocusAction</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+prevFocusAction</H3>
+<PRE>
+javax.swing.Action <B>prevFocusAction</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+buttonGroupSequences</H3>
+<PRE>
+javax.swing.ButtonGroup <B>buttonGroupSequences</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonCopy</H3>
+<PRE>
+javax.swing.JButton <B>jButtonCopy</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonCut</H3>
+<PRE>
+javax.swing.JButton <B>jButtonCut</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonDelete</H3>
+<PRE>
+javax.swing.JButton <B>jButtonDelete</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonExit</H3>
+<PRE>
+javax.swing.JButton <B>jButtonExit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonGo</H3>
+<PRE>
+javax.swing.JButton <B>jButtonGo</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonOpen</H3>
+<PRE>
+javax.swing.JButton <B>jButtonOpen</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonPaste</H3>
+<PRE>
+javax.swing.JButton <B>jButtonPaste</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonPrint</H3>
+<PRE>
+javax.swing.JButton <B>jButtonPrint</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jButtonSave</H3>
+<PRE>
+javax.swing.JButton <B>jButtonSave</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jComboBoxOutputFormat</H3>
+<PRE>
+javax.swing.JComboBox <B>jComboBoxOutputFormat</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jComboBoxScoringMatrix</H3>
+<PRE>
+javax.swing.JComboBox <B>jComboBoxScoringMatrix</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jFormattedTextFieldGapExtend</H3>
+<PRE>
+javax.swing.JFormattedTextField <B>jFormattedTextFieldGapExtend</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jFormattedTextFieldGapOpen</H3>
+<PRE>
+javax.swing.JFormattedTextField <B>jFormattedTextFieldGapOpen</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jLabelExtendGapPenalty</H3>
+<PRE>
+javax.swing.JLabel <B>jLabelExtendGapPenalty</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jLabelOpenGapPenalty</H3>
+<PRE>
+javax.swing.JLabel <B>jLabelOpenGapPenalty</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jLabelOutputFormat</H3>
+<PRE>
+javax.swing.JLabel <B>jLabelOutputFormat</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jLabelScoringMatrix</H3>
+<PRE>
+javax.swing.JLabel <B>jLabelScoringMatrix</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuBar</H3>
+<PRE>
+javax.swing.JMenuBar <B>jMenuBar</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuEdit</H3>
+<PRE>
+javax.swing.JMenu <B>jMenuEdit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuFile</H3>
+<PRE>
+javax.swing.JMenu <B>jMenuFile</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuHelp</H3>
+<PRE>
+javax.swing.JMenu <B>jMenuHelp</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemAbout</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemAbout</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemEditCopy</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemEditCopy</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemEditCut</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemEditCut</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemEditDelete</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemEditDelete</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemEditPaste</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemEditPaste</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemEditSelectAll</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemEditSelectAll</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemFileExit</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemFileExit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemFileLoadMatrix</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemFileLoadMatrix</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemFileLoadSequence1</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemFileLoadSequence1</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemFileLoadSequence2</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemFileLoadSequence2</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemFileOpen</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemFileOpen</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemFilePrint</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemFilePrint</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuItemToolsRunExample</H3>
+<PRE>
+javax.swing.JMenuItem <B>jMenuItemToolsRunExample</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jMenuTools</H3>
+<PRE>
+javax.swing.JMenu <B>jMenuTools</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelAlignment</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelAlignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelConsole</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelConsole</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelControls</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelControls</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelGapExtend</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelGapExtend</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelGapOpen</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelGapOpen</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelGo</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelGo</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelOutputFormat</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelOutputFormat</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelScoringMatrix</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelScoringMatrix</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelSequence1</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelSequence1</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPanelSequence2</H3>
+<PRE>
+javax.swing.JPanel <B>jPanelSequence2</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopup</H3>
+<PRE>
+javax.swing.JPopupMenu <B>jPopup</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupCopy</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupCopy</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupCut</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupCut</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupDelete</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupDelete</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupOpen</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupOpen</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupPaste</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupPaste</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupPrint</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupPrint</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupSave</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupSave</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupSelectAll</H3>
+<PRE>
+javax.swing.JMenuItem <B>jPopupSelectAll</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupSeparator1</H3>
+<PRE>
+javax.swing.JSeparator <B>jPopupSeparator1</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupSeparator2</H3>
+<PRE>
+javax.swing.JSeparator <B>jPopupSeparator2</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jPopupSeparator3</H3>
+<PRE>
+javax.swing.JSeparator <B>jPopupSeparator3</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jRadioButtonAlignment</H3>
+<PRE>
+javax.swing.JRadioButton <B>jRadioButtonAlignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jRadioButtonConsole</H3>
+<PRE>
+javax.swing.JRadioButton <B>jRadioButtonConsole</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jRadioButtonSequence1</H3>
+<PRE>
+javax.swing.JRadioButton <B>jRadioButtonSequence1</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jRadioButtonSequence2</H3>
+<PRE>
+javax.swing.JRadioButton <B>jRadioButtonSequence2</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jScrollPaneAlignment</H3>
+<PRE>
+javax.swing.JScrollPane <B>jScrollPaneAlignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jScrollPaneConsole</H3>
+<PRE>
+javax.swing.JScrollPane <B>jScrollPaneConsole</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jScrollPaneSequence1</H3>
+<PRE>
+javax.swing.JScrollPane <B>jScrollPaneSequence1</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jScrollPaneSequence2</H3>
+<PRE>
+javax.swing.JScrollPane <B>jScrollPaneSequence2</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jSeparatorFile</H3>
+<PRE>
+javax.swing.JSeparator <B>jSeparatorFile</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jSplitPaneBody</H3>
+<PRE>
+javax.swing.JSplitPane <B>jSplitPaneBody</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jSplitPaneIO</H3>
+<PRE>
+javax.swing.JSplitPane <B>jSplitPaneIO</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jSplitPaneSequences</H3>
+<PRE>
+javax.swing.JSplitPane <B>jSplitPaneSequences</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jTextAreaAlignment</H3>
+<PRE>
+javax.swing.JTextArea <B>jTextAreaAlignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jTextAreaSequence1</H3>
+<PRE>
+javax.swing.JTextArea <B>jTextAreaSequence1</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jTextAreaSequence2</H3>
+<PRE>
+javax.swing.JTextArea <B>jTextAreaSequence2</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jTextPaneConsole</H3>
+<PRE>
+javax.swing.JTextPane <B>jTextPaneConsole</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+jToolBar</H3>
+<PRE>
+javax.swing.JToolBar <B>jToolBar</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>jaligner.ui.filechooser</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.filechooser.FileChooserException"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/ui/filechooser/FileChooserException.html" title="class in jaligner.ui.filechooser">jaligner.ui.filechooser.FileChooserException</A> extends java.lang.Exception implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3258408434931086648l
+
+<P>
+
+<P>
+<A NAME="jaligner.ui.filechooser.NamedInputStream"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/ui/filechooser/NamedInputStream.html" title="class in jaligner.ui.filechooser">jaligner.ui.filechooser.NamedInputStream</A> extends java.lang.Object implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3256441404384686387l
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+name</H3>
+<PRE>
+java.lang.String <B>name</B></PRE>
+<DL>
+<DD>Name.
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+inputStream</H3>
+<PRE>
+java.io.InputStream <B>inputStream</B></PRE>
+<DL>
+<DD>Input stream.
+<P>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>jaligner.ui.util</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.ui.util.TextComponentUtilException"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/ui/util/TextComponentUtilException.html" title="class in jaligner.ui.util">jaligner.ui.util.TextComponentUtilException</A> extends java.lang.Exception implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>4050763797251567922l
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>jaligner.util</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="jaligner.util.SequenceParserException"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="jaligner/util/SequenceParserException.html" title="class in jaligner.util">jaligner.util.SequenceParserException</A> extends java.lang.Exception implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<B>serialVersionUID: </B>3258417248288191543l
+
+<P>
+
+<P>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="serialized-form.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+<table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Pub [...]
+</BODY>
+</HTML>
diff --git a/build.properties b/build.properties
new file mode 100644
index 0000000..6a089b0
--- /dev/null
+++ b/build.properties
@@ -0,0 +1,34 @@
+# The project name will be the name of the jar file.
+project.name = jaligner
+
+# CVS settings
+cvs.root = :pserver:anonymous at cvs1:/cvsroot/jaligner
+export.command = export -DNOW src
+
+# Where source files are found
+src.dir = ./src
+
+# Classpath
+class.path = ${classpath}:${java.home}/javaws/javaws.jar
+
+# Intermediate directory for building class files.
+build.dir = ./build
+
+# Compiler options.
+debug = on
+optimize = on
+deprecation = off
+packagename = jaligner
+
+# Javadoc options.
+javadoc.dir = ./api
+javadoc.style = jaligner.css
+javadoc.author = true
+javadoc.private = false
+javadoc.use = true
+javadoc.version = true
+javadoc.window.title = JAligner
+javadoc.doc.title = JAligner: Java implementation of Smith-Waterman algorithm for sequence alignment
+javadoc.header = <a href="http://jaligner.sourceforge.net">JAligner</a>
+javadoc.footer = <a href="http://jaligner.sourceforge.net">JAligner</a>
+javadoc.bottom = <table width="100%" border="0" cellpadding="0" cellspacing="0"><tr><td>Ahmed Moustafa (<a href="mailto:ahmed at users.sf.net">ahmed at users.sf.net</a>)</td><td align="right"><a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=88312&type=1" width="88" height="31" border="0" alt="SourceForge.net"></a></td></tr><tr colspan="2"><td><small>The source code of JAligner is licensed under <a href="http://www.opensource.org/licenses/gpl-license">Th [...]
diff --git a/build.xml b/build.xml
new file mode 100644
index 0000000..21a162f
--- /dev/null
+++ b/build.xml
@@ -0,0 +1,64 @@
+<project name="jaligner" default="build" basedir=".">
+ <property file="build.properties" />
+ <target name="clean" description="Delete the build directory">
+ <delete dir="${build.dir}" />
+ </target>
+ <target name="init" depends="clean">
+ <echo>JAVA_HOME: ${java.home}</echo>
+ <tstamp/>
+ <mkdir dir="${build.dir}" />
+ </target>
+ <target name="compile" depends="init"
+ description="Compile source code">
+ <javac srcdir="${src.dir}" destdir="${build.dir}"
+ debug="${debug}" optimize="${optimize}"
+ deprecation="${deprecation}" classpath="${class.path}">
+ <include name="**/*.java" />
+ </javac>
+ </target>
+ <target name="resources" depends="init"
+ description="Copy non-source code under the build directory">
+ <copy todir="build/jaligner/example/sequences">
+ <fileset dir="src/jaligner/example/sequences"></fileset>
+ </copy>
+ <copy todir="build/jaligner/matrix/matrices">
+ <fileset dir="src/jaligner/matrix/matrices"></fileset>
+ </copy>
+ <copy todir="build/jaligner/ui/images/gifs">
+ <fileset dir="src/jaligner/ui/images/gifs"></fileset>
+ </copy>
+ </target>
+ <target name="jar" depends="compile,resources">
+ <jar jarfile="${project.name}.jar" basedir="${build.dir}">
+ <manifest>
+ <attribute name="Main-Class"
+ value="jaligner.ui.AlignCommandLine" />
+ <attribute name="Created-At" value="${DSTAMP}${TSTAMP}"/>
+ </manifest>
+ </jar>
+ </target>
+ <target name="build" depends="jar,clean"
+ description="Build jar file" />
+ <target name="export" depends=""
+ description="Export source code from CVS repository">
+ <delete dir="${src.dir}" />
+ <cvs cvsRoot="${cvs.root}" command="${export.command}" />
+ </target>
+ <target name="run" depends="jar">
+ <java jar="jaligner.jar" classpath="${class.path}"
+ fork="true" />
+ </target>
+ <target name="javadoc" depends="init"
+ description="Generate API Javadocs">
+ <mkdir dir="${javadoc.dir}" />
+ <javadoc packagenames="${packagename}.*" sourcepath="src"
+ destdir="${javadoc.dir}" author="${javadoc.author}"
+ version="${javadoc.version}" use="${javadoc.use}"
+ private="${javadoc.private}"
+ windowtitle="${javadoc.window.title}"
+ doctitle="${javadoc.doc.title}" header="${javadoc.header}"
+ footer="${javadoc.footer}" bottom="${javadoc.bottom}"
+ stylesheetfile="${javadoc.style}" classpath="${class.path}">
+ </javadoc>
+ </target>
+</project>
diff --git a/jaligner.bat b/jaligner.bat
new file mode 100755
index 0000000..1738168
--- /dev/null
+++ b/jaligner.bat
@@ -0,0 +1 @@
+java -jar jaligner.jar
diff --git a/jaligner.css b/jaligner.css
new file mode 100644
index 0000000..6ec4b14
--- /dev/null
+++ b/jaligner.css
@@ -0,0 +1,38 @@
+/* ahmed.css -- default style sheet */
+
+BODY {
+color: black;
+background: white;
+font-family: Arial, Times, Courier, serif;
+margin-left: 2.5%;
+margin-right: 2.5%;
+<!-- font-size: 85%; -->
+}
+
+A:link {
+color: navy;
+text-decoration: none;
+}
+
+A:visited {
+color: purple;
+text-decoration: none;
+}
+
+A:hover {
+background: yellow;
+text-decoration: none;
+}
+
+A:active {
+background: cyan;
+text-decoration: none;
+}
+
+P, BLOCKQUOTE {
+text-align:justify;
+}
+
+UL {
+/*text-align:left;*/
+}
diff --git a/jaligner.jar b/jaligner.jar
new file mode 100644
index 0000000..25ec101
Binary files /dev/null and b/jaligner.jar differ
diff --git a/jaligner.sh b/jaligner.sh
new file mode 100755
index 0000000..1738168
--- /dev/null
+++ b/jaligner.sh
@@ -0,0 +1 @@
+java -jar jaligner.jar
diff --git a/src/NAligner/.cvsignore b/src/NAligner/.cvsignore
new file mode 100644
index 0000000..4e69665
--- /dev/null
+++ b/src/NAligner/.cvsignore
@@ -0,0 +1,13 @@
+bin
+obj
+doc
+Releases
+CVSROOT
+*.user
+*.suo
+*.idx
+*.mdx
+*.wdx
+_ReSharper*
+*resharper*
+
diff --git a/src/NAligner/Alignment.cs b/src/NAligner/Alignment.cs
new file mode 100644
index 0000000..cfb2a41
--- /dev/null
+++ b/src/NAligner/Alignment.cs
@@ -0,0 +1,244 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System;
+
+namespace NAligner
+{
+ /// <summary> Holds the output of a pairwise sequences alignment. </summary>
+ public class Alignment
+ {
+ /// <returns> Returns the extend. </returns>
+ public virtual float Extend
+ {
+ get { return extend; }
+ set { this.extend = value; }
+
+ }
+
+ /// <returns> Returns the matrix. </returns>
+ public virtual Matrix Matrix
+ {
+ get { return matrix; }
+ set { this.matrix = value; }
+
+ }
+
+ /// <returns> Returns the name1. </returns>
+ public virtual System.String Name1
+ {
+ get { return name1 == null || name1.Length == 0 ? DEFAULT_SEQUENCE1_NAME : name1; }
+ set { this.name1 = value; }
+
+ }
+
+ /// <returns> Returns the name2. </returns>
+ public virtual System.String Name2
+ {
+ get { return name2 == null || name2.Length == 0 ? DEFAULT_SEQUENCE2_NAME : name2; }
+
+ set { this.name2 = value; }
+
+ }
+
+ /// <returns> Returns the open. </returns>
+ public virtual float Open
+ {
+ get { return open; }
+ set { this.open = value; }
+
+ }
+
+ /// <returns> Returns the score. </returns>
+ public virtual float Score
+ {
+ get { return score; }
+ set { this.score = value; }
+
+ }
+
+ /// <returns> Returns the sequence1. </returns>
+ public virtual char[] Sequence1
+ {
+ get { return sequence1; }
+ set { this.sequence1 = value; }
+
+ }
+
+ /// <returns> Returns the sequence2. </returns>
+ public virtual char[] Sequence2
+ {
+ get { return sequence2; }
+ set { this.sequence2 = value; }
+
+ }
+
+ /// <returns> Returns the start1. </returns>
+ public virtual int Start1
+ {
+ get { return start1; }
+ set { this.start1 = value; }
+
+ }
+
+ /// <returns> Returns the start2. </returns>
+ public virtual int Start2
+ {
+ get { return start2; }
+ set { this.start2 = value; }
+
+ }
+
+ /// <returns> Returns the gaps. </returns>
+ public virtual int Gaps
+ {
+ get { return gaps; }
+ set { this.gaps = value; }
+
+ }
+
+ /// <returns> Returns the identity. </returns>
+ public virtual int Identity
+ {
+ get { return identity; }
+ set { this.identity = value; }
+
+ }
+
+ /// <returns> Returns the markupLine. </returns>
+ public virtual char[] MarkupLine
+ {
+ get { return markupLine; }
+ set { this.markupLine = value; }
+
+ }
+
+ /// <returns> Returns the similarity. </returns>
+ public virtual int Similarity
+ {
+ get { return similarity; }
+ set { this.similarity = value; }
+
+ }
+
+ /// <summary> Returns a summary for alignment</summary>
+ public virtual string Summary
+ {
+ get
+ {
+ throw new NotImplementedException("Unconverted part of the package.");
+
+// System.Text.StringBuilder buffer = new System.Text.StringBuilder();
+// //UPGRADE_ISSUE: Class 'java.text.DecimalFormat' was not converted. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1000_javatextDecimalFormat_3"'
+// //UPGRADE_ISSUE: Constructor 'java.text.DecimalFormat.DecimalFormat' was not converted. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1000_javatextDecimalFormat_3"'
+// DecimalFormat f1 = new DecimalFormat("0.00");
+// //UPGRADE_ISSUE: Class 'java.text.DecimalFormat' was not converted. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1000_javatextDecimalFormat_3"'
+// //UPGRADE_ISSUE: Constructor 'java.text.DecimalFormat.DecimalFormat' was not converted. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1000_javatextDecimalFormat_3"'
+// DecimalFormat f2 = new DecimalFormat("0.00%");
+//
+// int length = Sequence1.Length;
+//
+// buffer.Append("Sequence #1: " + Name1);
+// buffer.Append(Commons.LineSeparator);
+// buffer.Append("Sequence #2: " + Name2);
+// buffer.Append(Commons.LineSeparator);
+// buffer.Append("Matrix: " + (matrix.Id == null ? "" : matrix.Id));
+// buffer.Append(Commons.LineSeparator);
+// buffer.Append("Gap open: " + open);
+// buffer.Append(Commons.LineSeparator);
+// buffer.Append("Gap extend: " + extend);
+// buffer.Append(Commons.LineSeparator);
+// buffer.Append("Length: " + length);
+// buffer.Append(Commons.LineSeparator);
+// //UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1042_3"'
+// buffer.Append("Identity: " + identity + "/" + length + " (" + f2.FormatDouble(identity/(float) length) + ")");
+// buffer.Append(Commons.LineSeparator);
+// //UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1042_3"'
+// buffer.Append("Similarity: " + similarity + "/" + length + " (" + f2.FormatDouble(similarity/(float) length) + ")");
+// buffer.Append(Commons.LineSeparator);
+// //UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. 'ms-help://MS.VSCC.2003/commoner/redir/redirect.htm?keyword="jlca1042_3"'
+// buffer.Append("Gaps: " + gaps + "/" + length + " (" + f2.FormatDouble(gaps/(float) length) + ")");
+// buffer.Append(Commons.LineSeparator);
+// buffer.Append("Score: " + f1.FormatDouble(score));
+// buffer.Append(Commons.LineSeparator);
+//
+// return buffer.ToString();
+ }
+
+ }
+
+ /// <summary> Gap character</summary>
+ public const char GAP = '-';
+
+ /// <summary> Default name for sequence #1</summary>
+ private const System.String DEFAULT_SEQUENCE1_NAME = "jaligner_1";
+ /// <summary> Default name for sequence #2</summary>
+ private const System.String DEFAULT_SEQUENCE2_NAME = "jaligner_2";
+
+ /// <summary> Scoring matrix</summary>
+ private Matrix matrix;
+
+ /// <summary> Gap open cost</summary>
+ private float open;
+
+ /// <summary> Gap extend cost</summary>
+ private float extend;
+
+ /// <summary> Alignment score</summary>
+ private float score;
+
+ /// <summary> Aligned sequence #1</summary>
+ private char[] sequence1;
+
+ /// <summary> Name of sequence #1</summary>
+ private System.String name1;
+
+ /// <summary> Alignment start location in sequence #1</summary>
+ private int start1;
+
+ /// <summary> Aligned sequence #2</summary>
+ private char[] sequence2;
+
+ /// <summary> Name of sequence #2</summary>
+ private System.String name2;
+
+ /// <summary> Alignment start location in sequence #2</summary>
+ private int start2;
+
+ /// <summary> Markup line</summary>
+ private char[] markupLine;
+
+ /// <summary> Count of identical locations</summary>
+ private int identity;
+
+ /// <summary> Count of similar locations</summary>
+ private int similarity;
+
+ /// <summary> Count of gap locations</summary>
+ private int gaps;
+
+
+ /// <summary> Constructor for Alignment</summary>
+ public Alignment() : base()
+ {
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/AssemblyInfo.cs b/src/NAligner/AssemblyInfo.cs
new file mode 100644
index 0000000..9502454
--- /dev/null
+++ b/src/NAligner/AssemblyInfo.cs
@@ -0,0 +1,79 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System.Reflection;
+using System.Runtime.CompilerServices;
+
+// General Information about an assembly is controlled through the following
+// set of attributes. Change these attribute values to modify the information
+// associated with an assembly.
+
+[assembly : AssemblyTitle("NAligner")]
+[assembly : AssemblyDescription("C# port of the JAligner library")]
+[assembly : AssemblyCompany("")]
+[assembly : AssemblyProduct("")]
+[assembly : AssemblyCopyright("")]
+[assembly : AssemblyTrademark("")]
+[assembly : AssemblyCulture("")]
+
+
+// Version information for an assembly consists of the following four values:
+//
+// Major Version
+// Minor Version
+// Revision
+// Build Number
+//
+// You can specify all the values or you can default the Revision and Build Numbers
+// by using the '*' as shown below:
+
+[assembly : AssemblyVersion("0.1.*")]
+
+//
+// In order to sign your assembly you must specify a key to use. Refer to the
+// Microsoft .NET Framework documentation for more information on assembly signing.
+//
+// Use the attributes below to control which key is used for signing.
+//
+// Notes:
+// (*) If no key is specified, the assembly is not signed.
+// (*) KeyName refers to a key that has been installed in the Crypto Service
+// Provider (CSP) on your machine. KeyFile refers to a file which contains
+// a key.
+// (*) If the KeyFile and the KeyName values are both specified, the
+// following processing occurs:
+// (1) If the KeyName can be found in the CSP, that key is used.
+// (2) If the KeyName does not exist and the KeyFile does exist, the key
+// in the KeyFile is installed into the CSP and used.
+// (*) In order to create a KeyFile, you can use the sn.exe (Strong Name) utility.
+// When specifying the KeyFile, the location of the KeyFile should be
+// relative to the project output directory which is
+// %Project Directory%\obj\<configuration>. For example, if your KeyFile is
+// located in the project directory, you would specify the AssemblyKeyFile
+// attribute as [assembly: AssemblyKeyFile("..\..\mykey.snk")]
+// (*) Delay Signing is an advanced option - see the Microsoft .NET Framework
+// documentation for more information on this.
+//
+
+[assembly : AssemblyConfiguration("")]
+[assembly : AssemblyDelaySign(false)]
+[assembly : AssemblyKeyFile("")]
+[assembly : AssemblyKeyName("")]
\ No newline at end of file
diff --git a/src/NAligner/Cell.cs b/src/NAligner/Cell.cs
new file mode 100644
index 0000000..40a9589
--- /dev/null
+++ b/src/NAligner/Cell.cs
@@ -0,0 +1,75 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+namespace NAligner
+{
+ /// <summary> A cell in a similarity matrix, to hold row, column and score.</summary>
+ public class Cell
+ {
+ /// <summary> Gets or sets the column. </summary>
+ public virtual int Column
+ {
+ get { return this.column; }
+ set { this.column = value; }
+
+ }
+
+ /// <summary>Gets or sets the row.</summary>
+ public virtual int Row
+ {
+ get { return this.row; }
+ set { this.row = value; }
+
+ }
+
+ /// <summary>Gets or sets the score.</summary>
+ public virtual float Score
+ {
+ get { return this.score; }
+ set { this.score = value; }
+ }
+
+ /// <summary> Row of the cell</summary>
+ private int row;
+
+ /// <summary> Column of the cell</summary>
+ private int column;
+
+ /// <summary> Alignment score at this cell</summary>
+ private float score;
+
+ /// <summary> Constructor</summary>
+ public Cell() : base()
+ {
+ this.row = 0;
+ this.column = 0;
+ this.score = System.Single.NegativeInfinity;
+ }
+
+ /// <summary> Sets the row, column and score of the cell.</summary>
+ public virtual void Set(int row, int column, float score)
+ {
+ this.row = row;
+ this.column = column;
+ this.score = score;
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/Directions.cs b/src/NAligner/Directions.cs
new file mode 100644
index 0000000..04570ed
--- /dev/null
+++ b/src/NAligner/Directions.cs
@@ -0,0 +1,38 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+namespace NAligner
+{
+ // TODO: change Directions by an Enum
+
+ /// <summary> Traceback directions. </summary>
+ public abstract class Directions
+ {
+ /// <summary> Traceback direction stop</summary>
+ public const byte STOP = 0;
+ /// <summary> Traceback direction left</summary>
+ public const byte LEFT = 1;
+ /// <summary> Traceback direction diagonal</summary>
+ public const byte DIAGONAL = 2;
+ /// <summary> Traceback direction up</summary>
+ public const byte UP = 3;
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/Markups.cs b/src/NAligner/Markups.cs
new file mode 100644
index 0000000..ac8dead
--- /dev/null
+++ b/src/NAligner/Markups.cs
@@ -0,0 +1,39 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+namespace NAligner
+{
+ /// <summary> Markups line characters. </summary>
+ public abstract class Markups
+ {
+ /// <summary> Markup line identity character</summary>
+ public const char IDENTITY = '|';
+
+ /// <summary> Markup line similarity character</summary>
+ public const char SIMILARITY = ':';
+
+ /// <summary> Markup line gap character</summary>
+ public const char GAP = ' ';
+
+ /// <summary> Markup line mismatch character</summary>
+ public const char MISMATCH = '.';
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/Matrix.cs b/src/NAligner/Matrix.cs
new file mode 100644
index 0000000..fa82cd1
--- /dev/null
+++ b/src/NAligner/Matrix.cs
@@ -0,0 +1,117 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System;
+using System.IO;
+using NAligner.util;
+
+namespace NAligner
+{
+ /// <summary> Scoring matrix. </summary>
+ [Serializable]
+ public class Matrix
+ {
+ /// <summary> The starter character of a comment line.</summary>
+ private const char COMMENT_STARTER = '#';
+
+ /// <summary> The size of the scoring matrix. It is the number of the
+ /// characters in the ASCII table. It is more than the 20 amino acids just
+ /// to save the processing time of the mapping.</summary>
+ private const int SIZE = 127;
+
+ /// <summary> Matrix id (or name)</summary>
+ private string id = null;
+
+ /// <summary> Scores</summary>
+ private float[,] scores = null;
+
+ public Matrix(string id, float[,] scores)
+ {
+ this.id = id;
+ this.scores = scores;
+ }
+
+ /// <summary> Loads scoring matrix from a file.</summary>
+ /// <returns> loaded matrix </returns>
+ public static Matrix Load(string matrixPath)
+ {
+ char[] acids = new char[SIZE];
+
+ // Initialize the acids array to null values (ascii = 0)
+ for (int i = 0; i < SIZE; i++)
+ {
+ acids[i] = (char) (0);
+ }
+
+ float[,] scores = new float[SIZE, SIZE];
+
+ StreamReader reader = new StreamReader(matrixPath);
+
+ // Skip the comment lines
+ string line;
+ while ((line = reader.ReadLine()) != null && line.Trim()[0] == COMMENT_STARTER)
+ ;
+
+ // Read the headers line (the letters of the acids)
+ Tokenizer tokenizer = new Tokenizer(line.Trim());
+ for (int j = 0; tokenizer.HasMoreTokens(); j++)
+ {
+ acids[j] = tokenizer.NextToken()[0];
+ }
+
+ // Read the scores
+ while ((line = reader.ReadLine()) != null)
+ {
+ tokenizer = new Tokenizer(line.Trim());
+ char acid = tokenizer.NextToken()[0];
+ for (int i = 0; i < SIZE; i++)
+ {
+ if (acids[i] != 0)
+ {
+ scores[acid, acids[i]] = System.Single.Parse(tokenizer.NextToken());
+ }
+ }
+ }
+ return new Matrix(matrixPath, scores);
+ }
+
+ /// <returns> Returns the id. </returns>
+ public virtual string Id
+ {
+ get { return this.id; }
+
+ }
+
+ /// <returns> Returns the scores. </returns>
+ public virtual float[,] Scores
+ {
+ get { return this.scores; }
+
+ }
+
+
+ /// <returns> score </returns>
+ public virtual float GetScore(char a, char b)
+ {
+ return this.scores[a,b];
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/NAligner.csproj b/src/NAligner/NAligner.csproj
new file mode 100644
index 0000000..53450c5
--- /dev/null
+++ b/src/NAligner/NAligner.csproj
@@ -0,0 +1,189 @@
+<VisualStudioProject>
+ <CSHARP
+ ProjectType = "Local"
+ ProductVersion = "7.10.3077"
+ SchemaVersion = "2.0"
+ ProjectGuid = "{68BB6B9B-57B5-4E16-8B23-952CD406CE9B}"
+ >
+ <Build>
+ <Settings
+ ApplicationIcon = ""
+ AssemblyKeyContainerName = ""
+ AssemblyName = "NAligner"
+ AssemblyOriginatorKeyFile = ""
+ DefaultClientScript = "JScript"
+ DefaultHTMLPageLayout = "Grid"
+ DefaultTargetSchema = "IE50"
+ DelaySign = "false"
+ OutputType = "Library"
+ PreBuildEvent = ""
+ PostBuildEvent = ""
+ RootNamespace = "naligner"
+ RunPostBuildEvent = "OnBuildSuccess"
+ StartupObject = ""
+ >
+ <Config
+ Name = "Debug"
+ AllowUnsafeBlocks = "false"
+ BaseAddress = "285212672"
+ CheckForOverflowUnderflow = "false"
+ ConfigurationOverrideFile = ""
+ DefineConstants = "DEBUG;TESTS"
+ DocumentationFile = ""
+ DebugSymbols = "true"
+ FileAlignment = "4096"
+ IncrementalBuild = "true"
+ NoStdLib = "true"
+ NoWarn = ""
+ Optimize = "false"
+ OutputPath = "bin\Debug\"
+ RegisterForComInterop = "false"
+ RemoveIntegerChecks = "false"
+ TreatWarningsAsErrors = "false"
+ WarningLevel = "4"
+ />
+ <Config
+ Name = "Release"
+ AllowUnsafeBlocks = "false"
+ BaseAddress = "285212672"
+ CheckForOverflowUnderflow = "false"
+ ConfigurationOverrideFile = ""
+ DefineConstants = "RELEASE"
+ DocumentationFile = "bin\Release\NAligner.xml"
+ DebugSymbols = "true"
+ FileAlignment = "4096"
+ IncrementalBuild = "true"
+ NoStdLib = "true"
+ NoWarn = ""
+ Optimize = "false"
+ OutputPath = "bin\Release\"
+ RegisterForComInterop = "false"
+ RemoveIntegerChecks = "false"
+ TreatWarningsAsErrors = "false"
+ WarningLevel = "4"
+ />
+ </Settings>
+ <References>
+ <Reference
+ Name = "System"
+ AssemblyName = "System"
+ />
+ <Reference
+ Name = "System.Xml"
+ AssemblyName = "System.Xml"
+ />
+ <Reference
+ Name = "mscorlib"
+ AssemblyName = "mscorlib"
+ HintPath = "..\..\..\..\..\WINDOWS\Microsoft.NET\Framework\v1.1.4322\mscorlib.dll"
+ />
+ <Reference
+ Name = "nunit.framework"
+ AssemblyName = "nunit.framework"
+ HintPath = "..\..\..\..\..\Program Files\NUnit V2.1\\bin\nunit.framework.dll"
+ AssemblyFolderKey = "hklm\dn\nunit.framework"
+ />
+ </References>
+ </Build>
+ <Files>
+ <Include>
+ <File
+ RelPath = "Alignment.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "AssemblyInfo.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "Cell.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "Directions.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "Markups.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "Matrix.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "NamespaceDoc.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "Sequence.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "SmithWatermanGotoh.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "formats\AlignmentFormatter.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "formats\CLUSTAL.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "formats\FASTA.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "formats\FormatterFactory.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "formats\NamespaceDoc.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "formats\Pair.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "util\AlphanumericComparator.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "util\Commons.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "util\NAlignerException.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ <File
+ RelPath = "util\Tokenizer.cs"
+ SubType = "Code"
+ BuildAction = "Compile"
+ />
+ </Include>
+ </Files>
+ </CSHARP>
+</VisualStudioProject>
+
diff --git a/src/NAligner/NAligner.ndoc b/src/NAligner/NAligner.ndoc
new file mode 100644
index 0000000..4e9aaa0
--- /dev/null
+++ b/src/NAligner/NAligner.ndoc
@@ -0,0 +1,296 @@
+<project SchemaVersion="1.3">
+ <assemblies>
+ <assembly location="C:\Documents and Settings\Joannes Vermorel\My Documents\Visual Studio Projects\NAligner\bin\Release\NAligner.dll" documentation="C:\Documents and Settings\Joannes Vermorel\My Documents\Visual Studio Projects\NAligner\bin\Release\NAligner.xml" />
+ </assemblies>
+ <namespaces>
+ <namespace name="NAligner"></namespace>
+ <namespace name="NAligner.formats"></namespace>
+ <namespace name="NAligner.util"></namespace>
+ </namespaces>
+ <documenters>
+ <documenter name="JavaDoc">
+ <property name="Title" value="Math.NET Reference" />
+ <property name="OutputDirectory" value=".\doc\" />
+ <property name="ShowMissingSummaries" value="False" />
+ <property name="ShowMissingRemarks" value="False" />
+ <property name="ShowMissingParams" value="False" />
+ <property name="ShowMissingReturns" value="False" />
+ <property name="ShowMissingValues" value="False" />
+ <property name="DocumentExplicitInterfaceImplementations" value="False" />
+ <property name="DocumentInternals" value="False" />
+ <property name="DocumentProtected" value="True" />
+ <property name="DocumentSealedProtected" value="False" />
+ <property name="DocumentPrivates" value="False" />
+ <property name="DocumentProtectedInternalAsProtected" value="False" />
+ <property name="DocumentEmptyNamespaces" value="False" />
+ <property name="SkipNamespacesWithoutSummaries" value="False" />
+ <property name="EditorBrowsableFilter" value="Off" />
+ <property name="IncludeAssemblyVersion" value="False" />
+ <property name="CopyrightText" value="Copyright (c) 2004 - MathNet" />
+ <property name="CopyrightHref" value="" />
+ <property name="ReferencesPath" value="" />
+ <property name="FeedbackEmailAddress" value="" />
+ <property name="UseNamespaceDocSummaries" value="True" />
+ <property name="AutoPropertyBackerSummaries" value="False" />
+ <property name="AutoDocumentConstructors" value="True" />
+ <property name="GetExternalSummaries" value="True" />
+ <property name="Preliminary" value="False" />
+ <property name="UseNDocXmlFile" value="" />
+ <property name="CleanIntermediates" value="False" />
+ <property name="DocumentAttributes" value="False" />
+ <property name="ShowTypeIdInAttributes" value="False" />
+ <property name="DocumentedAttributes" value="" />
+ <property name="InheritPlatformSupport" value="True" />
+ <property name="DefaultOSSupport" value="all" />
+ <property name="SupportCompactFrameworkByDefault" value="False" />
+ <property name="SupportMONOFrameworkByDefault" value="False" />
+ <property name="AdditionalFrameworkList" value="" />
+ <property name="AdditionalOSList" value="" />
+ </documenter>
+ <documenter name="LaTeX">
+ <property name="OutputDirectory" value=".\doc\" />
+ <property name="TextFileFullName" value="Documentation.tex" />
+ <property name="TexFileBaseName" value="Documentation" />
+ <property name="LatexCompiler" value="latex" />
+ <property name="TexFileFullPath" value=".\doc\Documentation.tex" />
+ <property name="ShowMissingSummaries" value="False" />
+ <property name="ShowMissingRemarks" value="False" />
+ <property name="ShowMissingParams" value="False" />
+ <property name="ShowMissingReturns" value="False" />
+ <property name="ShowMissingValues" value="False" />
+ <property name="DocumentExplicitInterfaceImplementations" value="False" />
+ <property name="DocumentInternals" value="False" />
+ <property name="DocumentProtected" value="True" />
+ <property name="DocumentSealedProtected" value="False" />
+ <property name="DocumentPrivates" value="False" />
+ <property name="DocumentProtectedInternalAsProtected" value="False" />
+ <property name="DocumentEmptyNamespaces" value="False" />
+ <property name="SkipNamespacesWithoutSummaries" value="False" />
+ <property name="EditorBrowsableFilter" value="Off" />
+ <property name="IncludeAssemblyVersion" value="False" />
+ <property name="CopyrightText" value="" />
+ <property name="CopyrightHref" value="" />
+ <property name="ReferencesPath" value="" />
+ <property name="FeedbackEmailAddress" value="" />
+ <property name="UseNamespaceDocSummaries" value="False" />
+ <property name="AutoPropertyBackerSummaries" value="False" />
+ <property name="AutoDocumentConstructors" value="True" />
+ <property name="GetExternalSummaries" value="True" />
+ <property name="Preliminary" value="False" />
+ <property name="UseNDocXmlFile" value="" />
+ <property name="CleanIntermediates" value="False" />
+ <property name="DocumentAttributes" value="False" />
+ <property name="ShowTypeIdInAttributes" value="False" />
+ <property name="DocumentedAttributes" value="" />
+ <property name="InheritPlatformSupport" value="True" />
+ <property name="DefaultOSSupport" value="all" />
+ <property name="SupportCompactFrameworkByDefault" value="False" />
+ <property name="SupportMONOFrameworkByDefault" value="False" />
+ <property name="AdditionalFrameworkList" value="" />
+ <property name="AdditionalOSList" value="" />
+ </documenter>
+ <documenter name="LinearHtml">
+ <property name="IncludeTypeMemberDetails" value="False" />
+ <property name="OutputDirectory" value=".\doc\" />
+ <property name="MethodParametersInTable" value="False" />
+ <property name="TypeIncludeRegexp" value="" />
+ <property name="NamespaceExcludeRegexp" value="" />
+ <property name="Title" value="An NDoc Documented Class Library" />
+ <property name="IncludeHierarchy" value="False" />
+ <property name="SortTOCByNamespace" value="True" />
+ <property name="HeaderHtml" value="" />
+ <property name="FooterHtml" value="" />
+ <property name="FilesToInclude" value="" />
+ <property name="ShowMissingSummaries" value="False" />
+ <property name="ShowMissingRemarks" value="False" />
+ <property name="ShowMissingParams" value="False" />
+ <property name="ShowMissingReturns" value="False" />
+ <property name="ShowMissingValues" value="False" />
+ <property name="DocumentExplicitInterfaceImplementations" value="False" />
+ <property name="DocumentInternals" value="False" />
+ <property name="DocumentProtected" value="True" />
+ <property name="DocumentSealedProtected" value="False" />
+ <property name="DocumentPrivates" value="False" />
+ <property name="DocumentProtectedInternalAsProtected" value="False" />
+ <property name="DocumentEmptyNamespaces" value="False" />
+ <property name="SkipNamespacesWithoutSummaries" value="False" />
+ <property name="EditorBrowsableFilter" value="Off" />
+ <property name="IncludeAssemblyVersion" value="False" />
+ <property name="CopyrightText" value="" />
+ <property name="CopyrightHref" value="" />
+ <property name="ReferencesPath" value="" />
+ <property name="FeedbackEmailAddress" value="" />
+ <property name="UseNamespaceDocSummaries" value="False" />
+ <property name="AutoPropertyBackerSummaries" value="False" />
+ <property name="AutoDocumentConstructors" value="True" />
+ <property name="GetExternalSummaries" value="True" />
+ <property name="Preliminary" value="False" />
+ <property name="UseNDocXmlFile" value="" />
+ <property name="CleanIntermediates" value="False" />
+ <property name="DocumentAttributes" value="False" />
+ <property name="ShowTypeIdInAttributes" value="False" />
+ <property name="DocumentedAttributes" value="" />
+ <property name="InheritPlatformSupport" value="True" />
+ <property name="DefaultOSSupport" value="all" />
+ <property name="SupportCompactFrameworkByDefault" value="False" />
+ <property name="SupportMONOFrameworkByDefault" value="False" />
+ <property name="AdditionalFrameworkList" value="" />
+ <property name="AdditionalOSList" value="" />
+ </documenter>
+ <documenter name="MSDN">
+ <property name="OutputDirectory" value=".\doc\" />
+ <property name="HtmlHelpName" value="NAligner" />
+ <property name="IncludeFavorites" value="False" />
+ <property name="Title" value="NAligner library v0.1" />
+ <property name="DefaultTOC" value="" />
+ <property name="IncludeHierarchy" value="False" />
+ <property name="ShowVisualBasic" value="False" />
+ <property name="RootPageFileName" value="" />
+ <property name="RootPageContainsNamespaces" value="False" />
+ <property name="BinaryTOC" value="True" />
+ <property name="OutputTarget" value="HtmlHelpAndWeb" />
+ <property name="HeaderHtml" value="" />
+ <property name="FooterHtml" value="" />
+ <property name="FilesToInclude" value="" />
+ <property name="LinkToSdkDocVersion" value="SDK_v1_1" />
+ <property name="ExtensibilityStylesheet" value="" />
+ <property name="ShowMissingSummaries" value="False" />
+ <property name="ShowMissingRemarks" value="False" />
+ <property name="ShowMissingParams" value="False" />
+ <property name="ShowMissingReturns" value="False" />
+ <property name="ShowMissingValues" value="False" />
+ <property name="DocumentExplicitInterfaceImplementations" value="False" />
+ <property name="DocumentInternals" value="False" />
+ <property name="DocumentProtected" value="True" />
+ <property name="DocumentSealedProtected" value="False" />
+ <property name="DocumentPrivates" value="False" />
+ <property name="DocumentProtectedInternalAsProtected" value="False" />
+ <property name="DocumentEmptyNamespaces" value="False" />
+ <property name="SkipNamespacesWithoutSummaries" value="False" />
+ <property name="EditorBrowsableFilter" value="Off" />
+ <property name="IncludeAssemblyVersion" value="False" />
+ <property name="CopyrightText" value="" />
+ <property name="CopyrightHref" value="" />
+ <property name="ReferencesPath" value="" />
+ <property name="FeedbackEmailAddress" value="" />
+ <property name="UseNamespaceDocSummaries" value="True" />
+ <property name="AutoPropertyBackerSummaries" value="False" />
+ <property name="AutoDocumentConstructors" value="True" />
+ <property name="GetExternalSummaries" value="True" />
+ <property name="Preliminary" value="False" />
+ <property name="UseNDocXmlFile" value="" />
+ <property name="CleanIntermediates" value="False" />
+ <property name="DocumentAttributes" value="False" />
+ <property name="ShowTypeIdInAttributes" value="False" />
+ <property name="DocumentedAttributes" value="" />
+ <property name="InheritPlatformSupport" value="True" />
+ <property name="DefaultOSSupport" value="all" />
+ <property name="SupportCompactFrameworkByDefault" value="False" />
+ <property name="SupportMONOFrameworkByDefault" value="False" />
+ <property name="AdditionalFrameworkList" value="" />
+ <property name="AdditionalOSList" value="" />
+ </documenter>
+ <documenter name="VS.NET 2003">
+ <property name="OutputDirectory" value=".\doc\" />
+ <property name="HtmlHelpName" value="Documentation" />
+ <property name="Title" value="An NDoc documented library" />
+ <property name="IncludeHierarchy" value="False" />
+ <property name="RegisterTitleWithNamespace" value="False" />
+ <property name="CollectionNamespace" value="" />
+ <property name="RegisterTitleAsCollection" value="False" />
+ <property name="GenerateCollectionFiles" value="False" />
+ <property name="PlugInNamespace" value="ms.vscc" />
+ <property name="CollectionTOCStyle" value="Hierarchical" />
+ <property name="LinkToSdkDocVersion" value="SDK_v1_1" />
+ <property name="CharacterSet" value="UTF8" />
+ <property name="LangID" value="1033" />
+ <property name="BuildSeparateIndexFile" value="False" />
+ <property name="DocSetList" value="NETFramework" />
+ <property name="Version" value="1.0.0.0" />
+ <property name="CreateFullTextIndex" value="True" />
+ <property name="IncludeDefaultStopWordList" value="True" />
+ <property name="UseHelpNamespaceMappingFile" value="" />
+ <property name="OmitSyntaxSection" value="False" />
+ <property name="IntroductionPage" value="" />
+ <property name="AboutPageInfo" value="" />
+ <property name="EmptyIndexTermPage" value="" />
+ <property name="NavFailPage" value="" />
+ <property name="AboutPageIconPage" value="" />
+ <property name="AdditionalContentResourceDirectory" value="" />
+ <property name="ExtensibilityStylesheet" value="" />
+ <property name="ShowMissingSummaries" value="False" />
+ <property name="ShowMissingRemarks" value="False" />
+ <property name="ShowMissingParams" value="False" />
+ <property name="ShowMissingReturns" value="False" />
+ <property name="ShowMissingValues" value="False" />
+ <property name="DocumentExplicitInterfaceImplementations" value="False" />
+ <property name="DocumentInternals" value="False" />
+ <property name="DocumentProtected" value="True" />
+ <property name="DocumentSealedProtected" value="False" />
+ <property name="DocumentPrivates" value="False" />
+ <property name="DocumentProtectedInternalAsProtected" value="False" />
+ <property name="DocumentEmptyNamespaces" value="False" />
+ <property name="SkipNamespacesWithoutSummaries" value="False" />
+ <property name="EditorBrowsableFilter" value="Off" />
+ <property name="IncludeAssemblyVersion" value="False" />
+ <property name="CopyrightText" value="" />
+ <property name="CopyrightHref" value="" />
+ <property name="ReferencesPath" value="" />
+ <property name="FeedbackEmailAddress" value="" />
+ <property name="UseNamespaceDocSummaries" value="False" />
+ <property name="AutoPropertyBackerSummaries" value="False" />
+ <property name="AutoDocumentConstructors" value="True" />
+ <property name="GetExternalSummaries" value="True" />
+ <property name="Preliminary" value="False" />
+ <property name="UseNDocXmlFile" value="" />
+ <property name="CleanIntermediates" value="False" />
+ <property name="DocumentAttributes" value="False" />
+ <property name="ShowTypeIdInAttributes" value="False" />
+ <property name="DocumentedAttributes" value="" />
+ <property name="InheritPlatformSupport" value="True" />
+ <property name="DefaultOSSupport" value="all" />
+ <property name="SupportCompactFrameworkByDefault" value="False" />
+ <property name="SupportMONOFrameworkByDefault" value="False" />
+ <property name="AdditionalFrameworkList" value="" />
+ <property name="AdditionalOSList" value="" />
+ </documenter>
+ <documenter name="XML">
+ <property name="OutputFile" value=".\doc\doc.xml" />
+ <property name="ShowMissingSummaries" value="False" />
+ <property name="ShowMissingRemarks" value="False" />
+ <property name="ShowMissingParams" value="False" />
+ <property name="ShowMissingReturns" value="False" />
+ <property name="ShowMissingValues" value="False" />
+ <property name="DocumentExplicitInterfaceImplementations" value="False" />
+ <property name="DocumentInternals" value="False" />
+ <property name="DocumentProtected" value="True" />
+ <property name="DocumentSealedProtected" value="False" />
+ <property name="DocumentPrivates" value="False" />
+ <property name="DocumentProtectedInternalAsProtected" value="False" />
+ <property name="DocumentEmptyNamespaces" value="False" />
+ <property name="SkipNamespacesWithoutSummaries" value="False" />
+ <property name="EditorBrowsableFilter" value="Off" />
+ <property name="IncludeAssemblyVersion" value="False" />
+ <property name="CopyrightText" value="" />
+ <property name="CopyrightHref" value="" />
+ <property name="ReferencesPath" value="" />
+ <property name="FeedbackEmailAddress" value="" />
+ <property name="UseNamespaceDocSummaries" value="False" />
+ <property name="AutoPropertyBackerSummaries" value="False" />
+ <property name="AutoDocumentConstructors" value="True" />
+ <property name="GetExternalSummaries" value="True" />
+ <property name="Preliminary" value="False" />
+ <property name="UseNDocXmlFile" value="" />
+ <property name="CleanIntermediates" value="False" />
+ <property name="DocumentAttributes" value="False" />
+ <property name="ShowTypeIdInAttributes" value="False" />
+ <property name="DocumentedAttributes" value="" />
+ <property name="InheritPlatformSupport" value="True" />
+ <property name="DefaultOSSupport" value="all" />
+ <property name="SupportCompactFrameworkByDefault" value="False" />
+ <property name="SupportMONOFrameworkByDefault" value="False" />
+ <property name="AdditionalFrameworkList" value="" />
+ <property name="AdditionalOSList" value="" />
+ </documenter>
+ </documenters>
+</project>
\ No newline at end of file
diff --git a/src/NAligner/NamespaceDoc.cs b/src/NAligner/NamespaceDoc.cs
new file mode 100644
index 0000000..141595b
--- /dev/null
+++ b/src/NAligner/NamespaceDoc.cs
@@ -0,0 +1,36 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+namespace NAligner
+{
+ /// <summary>
+ /// <h3>NAligner</h3>
+ /// <p>Implementation of Smith-Waterman-Gotoh algorithm.</p>
+ /// <p>NAligner is a port of <a href="http://jaligner.sourceforge.net">JAligner</a>.</p>
+ /// <p/>
+ /// <p>Original author: Ahmed Moustafa (ahmed at users.sf.net).</p>
+ /// <p>.Net port by <a href="http://www.vermorel.com">Joannes Vermorel</a>.</p>
+ /// </summary>
+ public class NamespaceDoc
+ {
+ // for documentation only
+ }
+}
diff --git a/src/NAligner/Sequence.cs b/src/NAligner/Sequence.cs
new file mode 100644
index 0000000..5ab73e8
--- /dev/null
+++ b/src/NAligner/Sequence.cs
@@ -0,0 +1,283 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System;
+using System.IO;
+using System.Text;
+using NAligner.util;
+
+namespace NAligner
+{
+ public enum SequenceType
+ {
+ Protein,
+
+ Nucleic
+ }
+
+ /// <summary> A basic (nucleic or protein) sequence. It's a
+ /// wrapper to <c>string</c>. </summary>
+ /// <remarks>The <see cref="Sequence"/> can be parsed if encoded with
+ /// <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a>.</remarks>
+ [Serializable]
+ public class Sequence
+ {
+ /// <summary> Returns the sequence id</summary>
+ public virtual string Id
+ {
+ get { return id; }
+ set { this.id = value; }
+
+ }
+
+ /// <summary> Returns the sequence description</summary>
+ public virtual string Description
+ {
+ get { return description; }
+ set { this.description = value; }
+
+ }
+
+ /// <summary> Returns the sequence type (nucleic or protein) </summary>
+ public virtual SequenceType Type
+ {
+ get { return type; }
+ set { this.type = value; }
+
+ }
+
+// /// <summary> Sequence type nucleic.</summary>
+// public const int NUCLEIC = 0;
+//
+// /// <summary> Sequence type protein.</summary>
+// public const int PROTEIN = 1;
+
+ /// <summary> List of amino acids</summary>
+ private string aalist;
+
+ /// <summary> Sequence id.</summary>
+ private string id = null;
+
+ /// <summary> Sequence description.</summary>
+ private string description = null;
+
+ /// <summary> Sequence type.</summary>
+ private SequenceType type = SequenceType.Protein;
+
+ /// <summary> Constructor</summary>
+ public Sequence() : base()
+ {
+ }
+
+ /// <summary> Constructor</summary>
+ public Sequence(string sequence, string id, string description, SequenceType type) : base()
+ {
+ this.aalist = sequence;
+ this.id = id;
+ this.description = description;
+ this.type = type;
+ }
+
+ /// <summary> Gets or sets the amino acid sequence</summary>
+ public virtual string AAList
+ {
+ get { return aalist; }
+ set { this.aalist = value; }
+ }
+
+ public virtual int Length
+ {
+ get { return this.aalist.Length; }
+ }
+
+ /// <summary> Returns a subsequence</summary>
+ /// <param name="index">start index </param>
+ /// <param name="length">length of subsequence </param>
+ /// <returns> subsequence </returns>
+ public virtual string Subsequence(int index, int length)
+ {
+ return this.aalist.Substring(index, (index + length) - (index));
+ }
+
+ /// <summary> Returns the acid at specific location in the sequence</summary>
+ /// <param name="index">index </param>
+ /// <returns> acid at index </returns>
+ public virtual char AcidAt(int index)
+ {
+ return this.aalist[index];
+ }
+
+ /// <summary> Returns the sequence as an array of characters.</summary>
+ public virtual char[] ToArray()
+ {
+ return this.aalist.ToCharArray();
+ }
+
+ #region I/O
+
+ /// <summary> Returns a parsed Sequence from a FASTA string.</summary>
+ /// <param name="stringToParse">FASTA string to parse</param>
+ public static Sequence Parse(string stringToParse)
+ {
+ stringToParse = stringToParse.Replace("\r\n", "\n");
+
+ string sequenceName = null;
+ string sequenceDescription = null;
+
+ if (stringToParse.StartsWith(">"))
+ {
+ // FASTA format
+ int index = stringToParse.IndexOf("\n");
+
+ if (index == - 1)
+ {
+ throw new System.Exception("Invalid sequence");
+ }
+
+ string first = stringToParse.Substring(1, (index) - (1));
+ stringToParse = stringToParse.Substring(index);
+
+ index = 0;
+ for (int i = 0; i < first.Length && first[i] != ' ' && first[i] != '\t'; i++, index++)
+ {
+ // Skip white spaces
+ }
+ sequenceName = first.Substring(0, (index) - (0));
+ sequenceDescription = index + 1 > first.Length ? "" : first.Substring(index + 1);
+ }
+ else
+ {
+ // Plain format ... nothing to do here
+ }
+
+ Sequence s = new Sequence(PrepareAndValidate(stringToParse), sequenceName, sequenceDescription, SequenceType.Protein);
+
+ return s;
+ }
+
+ /// <summary> Returns a <see cref="Sequence"/> parsed and loaded from a file</summary>
+ /// <param name="file">to parse </param>
+ /// <returns> parsed sequence </returns>
+ public static Sequence Parse(FileInfo file)
+ {
+ string sequenceName = null;
+ string sequenceDescription = null;
+
+ StreamReader reader = new StreamReader(file.FullName);
+ StringBuilder buffer = new StringBuilder();
+
+ // Read & parse the first line
+ string line = reader.ReadLine();
+
+ if (line.StartsWith(">"))
+ {
+ // FASTA sequence
+
+ line = line.Substring(1).Trim();
+ int index = 0;
+ for (int i = 0; i < line.Length && line[i] != ' ' && line[i] != '\t'; i++, index++)
+ {
+ // Skip white spaces
+ }
+
+ sequenceName = line.Substring(0, (index) - (0));
+ sequenceDescription = index + 1 > line.Length ? "" : line.Substring(index + 1);
+ }
+ else
+ {
+ // Plain sequence
+ buffer.Append(PrepareAndValidate(line));
+ }
+
+ // Read the remaining the file (the actual sequence)
+ while ((line = reader.ReadLine()) != null)
+ {
+ buffer.Append(PrepareAndValidate(line));
+ }
+ reader.Close();
+
+ Sequence s = new Sequence(buffer.ToString(), sequenceName, sequenceDescription, SequenceType.Protein);
+ return s;
+ }
+
+ /// <summary> Removes whitespaces from a sequence and validates other characters.</summary>
+ /// <param name="stringToParse">sequence to be prepared</param>
+ /// <returns> prepared array of characters </returns>
+ private static string PrepareAndValidate(string stringToParse)
+ {
+ StringBuilder buffer = new StringBuilder();
+ string copy = stringToParse.Trim().ToUpper();
+
+ for (int i = 0, n = copy.Length; i < n; i++)
+ {
+ switch (copy[i])
+ {
+ // skip whitespaces
+ case (char) (9):
+ case (char) (10):
+ case (char) (13):
+ case (char) (32):
+ break;
+
+ // add a valid character
+
+ case 'A':
+ case 'B':
+ case 'C':
+ case 'D':
+ case 'E':
+ case 'F':
+ case 'G':
+ case 'H':
+ case 'I':
+ case 'K':
+ case 'L':
+ case 'M':
+ case 'N':
+ case 'P':
+ case 'Q':
+ case 'R':
+ case 'S':
+ case 'T':
+ case 'U':
+ case 'V':
+ case 'W':
+ case 'Y':
+ case 'Z':
+ case 'X':
+ case '-':
+ case '*':
+ buffer.Append(copy[i]);
+ break;
+
+ // throw an exception for anything else
+
+ default:
+ throw new NAlignerException("Invalid sequence character: " + copy[i]);
+
+ }
+ }
+ return buffer.ToString();
+ }
+
+ #endregion
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/SmithWatermanGotoh.cs b/src/NAligner/SmithWatermanGotoh.cs
new file mode 100644
index 0000000..22a04b0
--- /dev/null
+++ b/src/NAligner/SmithWatermanGotoh.cs
@@ -0,0 +1,416 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System;
+
+#if TESTS
+using System.IO;
+using NUnit.Framework;
+#endif
+
+namespace NAligner
+{
+ /// <summary> An implementation of the Smith-Waterman algorithm with
+ /// Gotoh's improvement for biological local pairwise sequence alignment. </summary>
+ public class SmithWatermanGotoh
+ {
+ /// <summary> Hidden constructor</summary>
+ private SmithWatermanGotoh() : base()
+ {
+ }
+
+ /// <summary> Aligns two sequences by Smith-Waterman algorithm</summary>
+ /// <param name="s1">sequene #1 </param>
+ /// <param name="s2">sequene #2 </param>
+ /// <param name="matrix">scoring matrix </param>
+ /// <param name="o">open gap penalty </param>
+ /// <param name="e">extend gap penalty </param>
+ /// <returns> alignment object contains the two aligned sequences,
+ /// the alignment score and alignment statistics</returns>
+ /// <seealso cref="Sequence"/>
+ /// <seealso cref="Matrix"/>
+ public static Alignment Align(Sequence s1, Sequence s2, Matrix matrix, float o, float e)
+ {
+ float[,] scores = matrix.Scores;
+
+ SmithWatermanGotoh sw = new SmithWatermanGotoh();
+
+ int m = s1.Length + 1;
+ int n = s2.Length + 1;
+
+ byte[] pointers = new byte[m * n];
+
+ // Initializes the boundaries of the traceback matrix to STOP.
+ for (int i = 0, k = 0; i < m; i++, k += n)
+ {
+ pointers[k] = Directions.STOP;
+ }
+ for (int j = 1; j < n; j++)
+ {
+ pointers[j] = Directions.STOP;
+ }
+
+ short[] sizesOfVerticalGaps = new short[m * n];
+ short[] sizesOfHorizontalGaps = new short[m * n];
+ for (int i = 0, k = 0; i < m; i++, k += n)
+ {
+ for (int j = 0; j < n; j++)
+ {
+ sizesOfVerticalGaps[k + j] = sizesOfHorizontalGaps[k + j] = 1;
+ }
+ }
+
+ Cell cell = sw.Construct(s1, s2, scores, o, e, pointers,
+ sizesOfVerticalGaps, sizesOfHorizontalGaps);
+
+ Alignment alignment = sw.Traceback(s1, s2, matrix, pointers, cell,
+ sizesOfVerticalGaps, sizesOfHorizontalGaps);
+
+ alignment.Name1 = s1.Id;
+ alignment.Name2 = s2.Id;
+ alignment.Matrix = matrix;
+ alignment.Open = o;
+ alignment.Extend = e;
+
+ return alignment;
+
+ }
+
+ /// <summary> Constructs directions matrix for the traceback </summary>
+ /// <param name="s1">sequence #1 </param>
+ /// <param name="s2">sequence #2 </param>
+ /// <param name="matrix">scoring matrix </param>
+ /// <param name="o">open gap penalty </param>
+ /// <param name="e">extend gap penalty </param>
+ /// <returns> The cell where the traceback starts. </returns>
+ private Cell Construct(Sequence s1, Sequence s2, float[,] matrix, float o,
+ float e, byte[] pointers, short[] sizesOfVerticalGaps, short[] sizesOfHorizontalGaps)
+ {
+
+ char[] a1 = s1.ToArray();
+ char[] a2 = s2.ToArray();
+
+ int m = s1.Length + 1;
+ int n = s2.Length + 1;
+
+ float f; // score of alignment x1...xi to y1...yi if xi aligns to yi
+ float[] g = new float[n]; // score if xi aligns to a gap after yi
+ float h; // score if yi aligns to a gap after xi
+ float[] v = new float[n]; // best score of alignment x1...xi to y1...yi
+ float vDiagonal;
+
+ g[0] = float.NegativeInfinity;
+ h = float.NegativeInfinity;
+ v[0] = 0;
+
+ for (int j = 1; j < n; j++)
+ {
+ g[j] = float.NegativeInfinity;
+ v[j] = 0;
+ }
+
+ float similarityScore, g1, g2, h1, h2;
+
+ Cell cell = new Cell();
+
+ for (int i = 1, k = n; i < m; i++, k += n)
+ {
+ h = float.NegativeInfinity;
+ vDiagonal = v[0];
+ for (int j = 1, l = k + 1; j < n; j++, l++)
+ {
+ similarityScore = matrix[a1[i - 1], a2[j - 1]];
+
+ // Fill the matrices
+ f = vDiagonal + similarityScore;
+
+ g1 = g[j] - e;
+ g2 = v[j] - o;
+ if (g1 > g2)
+ {
+ g[j] = g1;
+ sizesOfVerticalGaps[l] = (short) (sizesOfVerticalGaps[l - n] + 1);
+ }
+ else
+ {
+ g[j] = g2;
+ }
+
+ h1 = h - e;
+ h2 = v[j - 1] - o;
+ if (h1 > h2)
+ {
+ h = h1;
+ sizesOfHorizontalGaps[l] = (short) (sizesOfHorizontalGaps[l - 1] + 1);
+ }
+ else
+ {
+ h = h2;
+ }
+
+ vDiagonal = v[j];
+ v[j] = Max(f, g[j], h, 0);
+
+ // Determine the traceback direction
+ if (v[j] == 0)
+ {
+ pointers[l] = Directions.STOP;
+ }
+ else if (v[j] == f)
+ {
+ pointers[l] = Directions.DIAGONAL;
+ }
+ else if (v[j] == g[j])
+ {
+ pointers[l] = Directions.UP;
+ }
+ else
+ {
+ pointers[l] = Directions.LEFT;
+ }
+
+ // Set the traceback start at the current cell i, j and score
+ if (v[j] > cell.Score)
+ {
+ cell.Set(i, j, v[j]);
+ }
+ }
+ }
+
+ return cell;
+
+ }
+
+ /// <summary> Returns the alignment of two sequences based on the passed array of pointers</summary>
+ /// <param name="s1">sequence #1 </param>
+ /// <param name="s2">sequence #2 </param>
+ /// <param name="m">scoring matrix </param>
+ /// <param name="cell">The cell where the traceback starts. </param>
+ /// <returns> <see cref="Alignment"/> with the two aligned sequences and alignment score. </returns>
+ /// <seealso cref="Cell"/>
+ /// <seealso cref="Alignment"/>
+ private Alignment Traceback(Sequence s1, Sequence s2, Matrix m,
+ byte[] pointers, Cell cell, short[] sizesOfVerticalGaps, short[] sizesOfHorizontalGaps)
+ {
+
+ char[] a1 = s1.ToArray();
+ char[] a2 = s2.ToArray();
+
+ float[,] scores = m.Scores;
+
+ int n = s2.Length + 1;
+
+ Alignment alignment = new Alignment();
+ alignment.Score = cell.Score;
+
+ int maxlen = s1.Length + s2.Length; // maximum length after the
+ // aligned sequences
+
+ char[] reversed1 = new char[maxlen]; // reversed sequence #1
+ char[] reversed2 = new char[maxlen]; // reversed sequence #2
+ char[] reversed3 = new char[maxlen]; // reversed markup
+
+ int len1 = 0; // length of sequence #1 after alignment
+ int len2 = 0; // length of sequence #2 after alignment
+ int len3 = 0; // length of the markup line
+
+ int identity = 0; // count of identitcal pairs
+ int similarity = 0; // count of similar pairs
+ int gaps = 0; // count of gaps
+
+ char c1, c2;
+
+ int i = cell.Row; // traceback start row
+ int j = cell.Column; // traceback start col
+ int k = i * n;
+
+ bool stillGoing = true; // traceback flag: true -> continue & false
+ // -> stop
+
+ while (stillGoing)
+ {
+ switch (pointers[k + j])
+ {
+ case Directions.UP:
+
+ for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++)
+ {
+ reversed1[len1++] = a1[--i];
+ reversed2[len2++] = Alignment.GAP;
+ reversed3[len3++] = Markups.GAP;
+ k -= n;
+ gaps++;
+ }
+ break;
+
+ case Directions.DIAGONAL:
+ c1 = a1[--i];
+ c2 = a2[--j];
+ k -= n;
+ reversed1[len1++] = c1;
+ reversed2[len2++] = c2;
+ if (c1 == c2)
+ {
+ reversed3[len3++] = Markups.IDENTITY;
+ identity++;
+ similarity++;
+ }
+ else if (scores[c1,c2] > 0)
+ {
+ reversed3[len3++] = Markups.SIMILARITY;
+ similarity++;
+ }
+ else
+ {
+ reversed3[len3++] = Markups.MISMATCH;
+ }
+ break;
+
+ case Directions.LEFT:
+ for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++)
+ {
+ reversed1[len1++] = Alignment.GAP;
+ reversed2[len2++] = a2[--j];
+ reversed3[len3++] = Markups.GAP;
+ gaps++;
+ }
+ break;
+
+ case Directions.STOP:
+ stillGoing = false;
+ break;
+ }
+ }
+
+
+ alignment.Sequence1 = Reverse(reversed1, len1);
+ alignment.Start1 = i;
+ alignment.Sequence2 = Reverse(reversed2, len2);
+ alignment.Start2 = j;
+ alignment.MarkupLine = Reverse(reversed3, len3);
+ alignment.Identity = identity;
+ alignment.Gaps = gaps;
+ alignment.Similarity = similarity;
+
+ return alignment;
+
+ }
+
+ /// <summary> Returns the maximum of 4 float numbers.</summary>
+ private static float Max(float a, float b, float c, float d)
+ {
+ return Math.Max(Math.Max(a, b), Math.Max(c, d));
+ }
+
+ /// <summary> Reverses an array of chars</summary>
+ private static char[] Reverse(char[] a, int len)
+ {
+ // TODO: replace this method by System.Array.Reverse
+ char[] b = new char[len];
+ for (int i = len - 1, j = 0; i >= 0; i--, j++)
+ {
+ b[j] = a[i];
+ }
+ return b;
+ }
+
+#if TESTS
+ /// <summary>Testing the class <see cref="SmithWatermanGotoh"/>.</summary>
+ [TestFixture]
+ public class Tests
+ {
+ string NL = System.Environment.NewLine;
+
+ [Test] public void Align()
+ {
+ string matrixPath = @"../../matrices/PAM250";
+ if(!File.Exists(matrixPath)) matrixPath = @"PAM250";
+
+ Matrix pam250 = Matrix.Load(matrixPath);
+
+ float opengap = 15.0f;
+ float extendgap = 3.0f;
+
+ string str1 = @">100K_RAT 100 kDa protein (EC 6.3.2.-)." + NL +
+ "MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT" +
+ "PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM" +
+ "TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA GSGKCLVEVT" +
+ "MDRNCLEVLP TKMSYAANLK NVMNMQNRQK KAGEDQSMLA EEADSSKPGP SAHDVAAQLK" +
+ "SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG" +
+ "SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT" +
+ "TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLDCIQNAN KGTHTSLMQR" +
+ "LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPDP" +
+ "LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVEEAMELI" +
+ "VAHGRENGAD SILDLGLLDS SEKVQENRKR HGSSRSVVDM DLDDTDDGDD NAPLFYQPGK" +
+ "RGFYTPRPGK NTEARLNCFR NIGRILGLCL LQNELCPITL NRHVIKVLLG RKVNWHDFAF" +
+ "FDPVMYESLR QLILASQSSD ADAVFSAMDL AFAVDLCKEE GGGQVELIPN GVNIPVTPQN" +
+ "VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML" +
+ "ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP" +
+ "SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV";
+
+ string str2 = @">104K_THEPA 104 kDa microneme-rhoptry antigen." + NL +
+ "MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL" +
+ "QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG" +
+ "DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN" +
+ "GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK" +
+ "YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI" +
+ "TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT" +
+ "THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS" +
+ "EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT" +
+ "QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS" +
+ "SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR" +
+ "PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD" +
+ "DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK" +
+ "DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR" +
+ "SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL" +
+ "TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP" +
+ "KKPDSAYIPS ILAILVVSLI VGIL";
+
+
+ Sequence seq1 = Sequence.Parse(str1);
+ Sequence seq2 = Sequence.Parse(str2);
+
+ Alignment alignment = SmithWatermanGotoh.Align(seq1, seq2, pam250, opengap, extendgap);
+
+ Assert.AreEqual(98.0f, alignment.Score, "Unexpected score.");
+ }
+
+ [Test] public void Align2()
+ {
+ string matrixPath = @"../../matrices/TEST1";
+ if(!File.Exists(matrixPath)) matrixPath = @"TEST1";
+
+ Matrix customMatrix = Matrix.Load(matrixPath);
+
+ Sequence seq1 = Sequence.Parse(@"AACCC");
+ Sequence seq2 = Sequence.Parse(@"CCACC");
+
+ float opengap = 2.0f;
+ float extendgap = 1.0f;
+
+ Alignment alignment = SmithWatermanGotoh.Align(seq1, seq2, customMatrix, opengap, extendgap);
+
+ Assert.AreEqual(14.0f, alignment.Score, "Unexpected score.");
+ }
+ }
+#endif
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/formats/AlignmentFormatter.cs b/src/NAligner/formats/AlignmentFormatter.cs
new file mode 100644
index 0000000..fcc6ccb
--- /dev/null
+++ b/src/NAligner/formats/AlignmentFormatter.cs
@@ -0,0 +1,44 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using NAligner;
+
+namespace NAligner.formats
+{
+ /// <summary> Abstract format </summary>
+ public abstract class AlignmentFormatter
+ {
+ /// <summary> Gets or sets format id</summary>
+ public virtual string Id
+ {
+ get { return this.id == null ? this.GetType().FullName : this.id; }
+ set { this.id = value; }
+
+ }
+
+ /// <summary> Formatter id </summary>
+ private string id = null;
+
+ /// <summary> Formats alignment</summary>
+ /// <returns> formatted alignment </returns>
+ public abstract string Format(Alignment alignment);
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/formats/CLUSTAL.cs b/src/NAligner/formats/CLUSTAL.cs
new file mode 100644
index 0000000..60f8f0f
--- /dev/null
+++ b/src/NAligner/formats/CLUSTAL.cs
@@ -0,0 +1,117 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System.Text;
+using NAligner;
+
+namespace NAligner.formats
+{
+ /// <summary> <p>CLUSTAL format.</p>
+ /// Example:
+ /// <code>
+ /// CLUSTAL_FORMAT W(1.60) multiple sequence alignment
+ ///
+ ///
+ /// JC2395 NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
+ /// KPEL_DROME MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
+ /// FASA_MOUSE NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
+ ///
+ ///
+ /// JC2395 -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
+ /// KPEL_DROME -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
+ /// FASA_MOUSE -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
+ ///
+ ///
+ /// JC2395 IAEEIQAM
+ /// KPEL_DROME AMRLIKDY
+ /// FASA_MOUSE TLDKFQDM
+ /// </code>
+ ///
+ /// </summary>
+ /// <author> Ahmed Moustafa (ahmed at users.sf.net) </author>
+ public class CLUSTAL : AlignmentFormatter
+ {
+ /// <summary> Name width </summary>
+ private const int NAME_WIDTH = 36;
+
+ /// <summary> Sequence width</summary>
+ private const int SEQUENCE_WIDTH = 50;
+
+ /// <summary> CLUSTAL header</summary>
+ private const string HEADER = "CLUSTAL_FORMAT W(1.60) multiple sequence alignment\n\n";
+
+ /// <summary> Constructor</summary>
+ public CLUSTAL() : base()
+ {
+ Id = "CLUSTAL";
+ }
+
+ /// <summary> Returns CLUSTAL format</summary>
+ /// <param name="names">array of the names of the sequences.</param>
+ /// <param name="sequences">array of the sequences</param>
+ public virtual string Format(string[] names, string[] sequences)
+ {
+ StringBuilder buffer = new StringBuilder(HEADER);
+ int maxSequenceLength = 0;
+ for (int i = 0; i < sequences.Length; i++)
+ {
+ if (sequences[i].Length > maxSequenceLength)
+ {
+ maxSequenceLength = sequences[i].Length;
+ }
+ }
+
+ for (int i = 0; i*SEQUENCE_WIDTH < maxSequenceLength; i++)
+ {
+ for (int j = 0; j < sequences.Length; j++)
+ {
+ buffer.Append(NAME_WIDTH <= names[j].Length ? names[j].Substring(0, (NAME_WIDTH - 1) - (0)) : names[j]);
+ for (int k = names[j].Length; k < NAME_WIDTH; k++)
+ {
+ buffer.Append(" ");
+ }
+ if (names[j].Length >= NAME_WIDTH)
+ {
+ buffer.Append(" ");
+ }
+ buffer.Append(sequences[j].Substring(i*SEQUENCE_WIDTH, (((i + 1)*SEQUENCE_WIDTH) < sequences[j].Length ? (i + 1)*SEQUENCE_WIDTH : sequences[j].Length) - (i*SEQUENCE_WIDTH)));
+ if (j < sequences.Length)
+ {
+ buffer.Append("\n");
+ }
+ }
+ if ((i + 1)*SEQUENCE_WIDTH < maxSequenceLength)
+ {
+ buffer.Append("\n\n");
+ }
+ }
+ return buffer.ToString();
+ }
+
+ /// <summary> Returns CLUSTAL format of the alignment</summary>
+ public override string Format(Alignment alignment)
+ {
+ string[] sequences = new string[] {new string(alignment.Sequence1), new string(alignment.Sequence2)};
+ string[] names = new string[] {alignment.Name1, alignment.Name2};
+ return Format(names, sequences);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/formats/FASTA.cs b/src/NAligner/formats/FASTA.cs
new file mode 100644
index 0000000..15d3b75
--- /dev/null
+++ b/src/NAligner/formats/FASTA.cs
@@ -0,0 +1,70 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System.Text;
+using NAligner;
+
+namespace NAligner.formats
+{
+ /// <summary> <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> formatter</summary>
+ public class FASTA : AlignmentFormatter
+ {
+ /// <summary> Number of characters per line</summary>
+ private const int LINE_WIDTH = 60;
+
+ /// <summary> Constructor for FASTA.</summary>
+ public FASTA() : base()
+ {
+ Id = "FASTA";
+ }
+
+ /// <summary> Returns the name, description and sequence combined in one string.
+ /// The length of each line in the sequence is FASTA.LINE_LENGTH</summary>
+ public virtual string Format(Sequence sequence)
+ {
+ StringBuilder buffer = new StringBuilder(">");
+ buffer.Append(sequence.Id == null ? "" : sequence.Id);
+ buffer.Append("\n");
+ for (int i = 0, n = sequence.Length; i*LINE_WIDTH < n; i++)
+ {
+ for (int j = i*LINE_WIDTH, m = (i + 1)*LINE_WIDTH < n ? (i + 1)*LINE_WIDTH : n; j < m; j++)
+ {
+ buffer.Append(sequence.Subsequence(j, 1));
+ }
+ buffer.Append("\n");
+ }
+ return buffer.ToString();
+ }
+
+ /// <returns> FASTA format of the input alignment</returns>
+ public override string Format(Alignment alignment)
+ {
+ System.Text.StringBuilder buffer = new System.Text.StringBuilder();
+ System.Text.StringBuilder s1 = new System.Text.StringBuilder();
+ System.Text.StringBuilder s2 = new System.Text.StringBuilder();
+ s1.Append(alignment.Sequence1);
+ s2.Append(alignment.Sequence2);
+ buffer.Append(Format(new Sequence(s1.ToString(), alignment.Name1, "", SequenceType.Protein)));
+ buffer.Append(Format(new Sequence(s2.ToString(), alignment.Name2, "", SequenceType.Protein)));
+ return buffer.ToString();
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/formats/FormatterFactory.cs b/src/NAligner/formats/FormatterFactory.cs
new file mode 100644
index 0000000..e56eedd
--- /dev/null
+++ b/src/NAligner/formats/FormatterFactory.cs
@@ -0,0 +1,72 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System.Collections;
+
+namespace NAligner.formats
+{
+ /// <summary> Singleton formatter factory. </summary>
+ public class FormatterFactory
+ {
+ /// <summary> Returns the singleton instance for <see cref="FormatterFactory"/>.</summary>
+ public static FormatterFactory Default
+ {
+ get
+ {
+ if (singletonInstance == null)
+ {
+ singletonInstance = new FormatterFactory();
+ }
+ return singletonInstance;
+ }
+
+ }
+
+ /// <summary> Returns a list of registered formatters</summary>
+ public virtual ICollection Formatters
+ {
+ get { return formats.Keys; }
+ }
+
+ private static FormatterFactory singletonInstance = null;
+
+ /// <summary>Table containing the <see cref="AlignmentFormatter"/>s.</summary>
+ private Hashtable formats = new Hashtable();
+
+ /// <summary> Hidden constructor </summary>
+ private FormatterFactory() : base()
+ {
+ }
+
+ /// <summary> Registers a new formatter.</summary>
+ public virtual void RegisterFormatter(AlignmentFormatter alignmentFormatter)
+ {
+ formats[alignmentFormatter.Id] = alignmentFormatter;
+ }
+
+ /// <summary> Returns a <see cref="AlignmentFormatter"/>.</summary>
+ /// <param name="id">formatter id </param>
+ public virtual AlignmentFormatter GetFormatter(string id)
+ {
+ return (AlignmentFormatter) formats[id];
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/formats/NamespaceDoc.cs b/src/NAligner/formats/NamespaceDoc.cs
new file mode 100644
index 0000000..8007265
--- /dev/null
+++ b/src/NAligner/formats/NamespaceDoc.cs
@@ -0,0 +1,29 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+namespace NAligner.formats
+{
+ /// <summary>Group of formats for output alignments.</summary>
+ public class NamespaceDoc
+ {
+ // for documentation only
+ }
+}
diff --git a/src/NAligner/formats/Pair.cs b/src/NAligner/formats/Pair.cs
new file mode 100644
index 0000000..42f8052
--- /dev/null
+++ b/src/NAligner/formats/Pair.cs
@@ -0,0 +1,189 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System.Text;
+using NAligner;
+using NAligner.util;
+
+namespace NAligner.formats
+{
+ /// <summary>
+ /// <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.</summary>
+ public class Pair : AlignmentFormatter
+ {
+ /// <summary> Name width </summary>
+ private const int NAME_WIDTH = 13;
+
+ /// <summary> Position width</summary>
+ private const int POSITION_WIDTH = 6;
+
+ /// <summary> Sequence width</summary>
+ private const int SEQUENCE_WIDTH = 50;
+
+ /// <summary> Space</summary>
+ private const string BLANK = " ";
+
+ /// <summary> Constructor </summary>
+ public Pair() : base()
+ {
+ Id = "Pair";
+ }
+
+ /// <summary> Formats an alignment object to the Pair_FORMAT format</summary>
+ /// <param name="alignment">alignment object to be formated </param>
+ /// <returns> string of the alignment pair-formatted </returns>
+ public override string Format(Alignment alignment)
+ {
+ char[] sequence1 = alignment.Sequence1;
+ char[] sequence2 = alignment.Sequence2;
+ char[] markup = alignment.MarkupLine;
+
+ int length = sequence1.Length > sequence2.Length ? sequence2.Length : sequence1.Length;
+
+ string name1 = AdjustName(alignment.Name1);
+ string name2 = AdjustName(alignment.Name2);
+
+ StringBuilder buffer = new StringBuilder();
+
+ StringBuilder preMarkup = new StringBuilder();
+ for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++)
+ {
+ preMarkup.Append(BLANK);
+ }
+
+ int oldPosition1, position1 = 1 + alignment.Start1;
+ int oldPosition2, position2 = 1 + alignment.Start2;
+
+ char[] subsequence1;
+ char[] subsequence2;
+ char[] submarkup;
+ int line;
+
+ char c1, c2;
+
+ for (int i = 0; i*SEQUENCE_WIDTH < length; i++)
+ {
+ oldPosition1 = position1;
+ oldPosition2 = position2;
+
+ line = ((i + 1)*SEQUENCE_WIDTH) < length ? (i + 1)*SEQUENCE_WIDTH : length;
+
+ subsequence1 = new char[line - i*SEQUENCE_WIDTH];
+ subsequence2 = new char[line - i*SEQUENCE_WIDTH];
+ submarkup = new char[line - i*SEQUENCE_WIDTH];
+
+ for (int j = i*SEQUENCE_WIDTH, k = 0; j < line; j++, k++)
+ {
+ subsequence1[k] = sequence1[j];
+ subsequence2[k] = sequence2[j];
+ submarkup[k] = markup[j];
+ c1 = subsequence1[k];
+ c2 = subsequence2[k];
+ if (c1 == c2)
+ {
+ position1++;
+ position2++;
+ }
+ else if (c1 == Alignment.GAP)
+ {
+ position2++;
+ }
+ else if (c2 == Alignment.GAP)
+ {
+ position1++;
+ }
+ else
+ {
+ position1++;
+ position2++;
+ }
+ }
+
+ buffer.Append(name1);
+ buffer.Append(BLANK);
+ buffer.Append(AdjustPosition((oldPosition1).ToString()));
+ buffer.Append(BLANK);
+ buffer.Append(subsequence1);
+ buffer.Append(BLANK);
+ buffer.Append(AdjustPosition(((position1 - 1)).ToString()));
+ buffer.Append(Commons.LineSeparator);
+
+ buffer.Append(preMarkup);
+ buffer.Append(submarkup);
+ buffer.Append(Commons.LineSeparator);
+
+ buffer.Append(name2);
+ buffer.Append(BLANK);
+ buffer.Append(AdjustPosition((oldPosition2).ToString()));
+ buffer.Append(BLANK);
+ buffer.Append(subsequence2);
+ buffer.Append(BLANK);
+ buffer.Append(AdjustPosition(((position2 - 1)).ToString()));
+ buffer.Append(Commons.LineSeparator);
+
+ buffer.Append(Commons.LineSeparator);
+ }
+ return buffer.ToString();
+ }
+
+ private string AdjustName(string name)
+ {
+ System.Text.StringBuilder buffer = new System.Text.StringBuilder();
+
+ if (name.Length > NAME_WIDTH)
+ {
+ buffer.Append(name.Substring(0, (NAME_WIDTH) - (0)));
+ }
+ else
+ {
+ buffer.Append(name);
+ for (int j = buffer.Length; j < NAME_WIDTH; j++)
+ {
+ buffer.Append(BLANK);
+ }
+ }
+ return buffer.ToString();
+ }
+
+ private string AdjustPosition(string position)
+ {
+ System.Text.StringBuilder buffer1 = new System.Text.StringBuilder();
+ System.Text.StringBuilder buffer2 = new System.Text.StringBuilder();
+
+ if (position.Length > POSITION_WIDTH)
+ {
+ buffer1.Append(position.Substring(position.Length - POSITION_WIDTH, (position.Length) - (position.Length - POSITION_WIDTH)));
+ }
+ else
+ {
+ buffer1.Append(position);
+ }
+
+ for (int j = 0, n = POSITION_WIDTH - buffer1.Length; j < n; j++)
+ {
+ buffer2.Append(BLANK);
+ }
+
+ buffer2.Append(buffer1.ToString());
+ return buffer2.ToString();
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/matrices/BLOSUM100 b/src/NAligner/matrices/BLOSUM100
new file mode 100644
index 0000000..46e9e85
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM100
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum100_3.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 100
+# Entropy = 1.4516, Expected = -1.0948
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10
+R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10
+N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10
+D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10
+C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10
+Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10
+E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10
+G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10
+H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10
+I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10
+L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10
+K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10
+M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10
+F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10
+P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10
+S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10
+T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10
+W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10
+Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10
+V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10
+B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10
+Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10
+X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/BLOSUM30 b/src/NAligner/matrices/BLOSUM30
new file mode 100644
index 0000000..81ebd98
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM30
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum30.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/5 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 30
+# Entropy = 0.1424, Expected = -0.1074
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7
+R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7
+N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7
+D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7
+C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7
+Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7
+E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7
+G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7
+H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7
+I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7
+L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7
+K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7
+M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7
+F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7
+P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7
+S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7
+T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7
+W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7
+Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7
+V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7
+B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7
+Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7
+X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/NAligner/matrices/BLOSUM35 b/src/NAligner/matrices/BLOSUM35
new file mode 100644
index 0000000..a6d99f5
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM35
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum35.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 35
+# Entropy = 0.2111, Expected = -0.1550
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5
+R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5
+N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5
+D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5
+C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5
+Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5
+E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5
+G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5
+H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5
+I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5
+L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5
+K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5
+M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5
+F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5
+P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5
+S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5
+T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5
+W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5
+Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5
+V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5
+B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5
+Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5
+X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM40 b/src/NAligner/matrices/BLOSUM40
new file mode 100644
index 0000000..1a4baa2
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM40
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum40.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 40
+# Entropy = 0.2851, Expected = -0.2090
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6
+R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6
+N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6
+D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6
+C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6
+Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6
+E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6
+G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6
+H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6
+I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6
+L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6
+K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6
+M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6
+F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6
+P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6
+S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6
+T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6
+W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6
+Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6
+V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6
+B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6
+Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/src/NAligner/matrices/BLOSUM45 b/src/NAligner/matrices/BLOSUM45
new file mode 100644
index 0000000..18c3323
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM45
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum45.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 45
+# Entropy = 0.3795, Expected = -0.2789
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5
+R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
+N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
+D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5
+Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
+E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5
+G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5
+H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5
+I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5
+L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5
+K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5
+M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5
+F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5
+P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5
+Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5
+V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5
+B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
+Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM50 b/src/NAligner/matrices/BLOSUM50
new file mode 100644
index 0000000..3f62e3c
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM50
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum50.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 50
+# Entropy = 0.4808, Expected = -0.3573
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5
+N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5
+D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5
+C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5
+Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5
+E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5
+G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5
+H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5
+I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5
+L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5
+K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5
+M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5
+F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5
+P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5
+S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5
+W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5
+Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5
+V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5
+B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5
+Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5
+X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM55 b/src/NAligner/matrices/BLOSUM55
new file mode 100644
index 0000000..c0cf3ff
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM55
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum55.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 55
+# Entropy = 0.5637, Expected = -0.4179
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5
+R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5
+D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5
+C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5
+Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
+E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5
+G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5
+H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5
+I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5
+L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5
+K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5
+M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
+F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5
+P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5
+S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5
+W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5
+Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5
+V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5
+B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5
+Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5
+X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM60 b/src/NAligner/matrices/BLOSUM60
new file mode 100644
index 0000000..4fd1943
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM60
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum60.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 60
+# Entropy = 0.6603, Expected = -0.4917
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
+R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4
+N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
+D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
+C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
+E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4
+L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4
+K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4
+V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
+B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4
+Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/src/NAligner/matrices/BLOSUM62 b/src/NAligner/matrices/BLOSUM62
new file mode 100644
index 0000000..205f139
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM62
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum62.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 62
+# Entropy = 0.6979, Expected = -0.5209
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
+R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
+N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
+D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
+C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
+V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
+B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
+Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/src/NAligner/matrices/BLOSUM65 b/src/NAligner/matrices/BLOSUM65
new file mode 100644
index 0000000..1eacd14
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM65
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum65.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 65
+# Entropy = 0.7576, Expected = -0.5675
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5
+D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5
+C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5
+Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5
+G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5
+H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5
+L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5
+M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
+F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5
+P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5
+Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5
+V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5
+B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5
+Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5
+X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM70 b/src/NAligner/matrices/BLOSUM70
new file mode 100644
index 0000000..3e4093f
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM70
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum70.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 70
+# Entropy = 0.8391, Expected = -0.6313
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5
+D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5
+C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5
+Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5
+E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
+G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
+H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5
+I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5
+L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5
+M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
+F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
+P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5
+S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5
+Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5
+V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5
+B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5
+Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5
+X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM75 b/src/NAligner/matrices/BLOSUM75
new file mode 100644
index 0000000..98964be
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM75
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum75.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 75
+# Entropy = 0.9077, Expected = -0.6845
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5
+D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5
+C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5
+Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5
+E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
+G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
+H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5
+I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5
+L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5
+M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5
+F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
+P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5
+S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5
+Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5
+V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5
+B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5
+Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5
+X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/NAligner/matrices/BLOSUM80 b/src/NAligner/matrices/BLOSUM80
new file mode 100644
index 0000000..78172a3
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM80
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum80_3.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 80
+# Entropy = 0.9868, Expected = -0.7442
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8
+R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8
+N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8
+D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8
+C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8
+Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8
+E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8
+G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8
+H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8
+I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8
+L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8
+K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8
+M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8
+F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8
+P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8
+S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8
+T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8
+W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8
+Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8
+V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8
+B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8
+Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8
+X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/BLOSUM85 b/src/NAligner/matrices/BLOSUM85
new file mode 100644
index 0000000..cb47fd2
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM85
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum85.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 85
+# Entropy = 1.0805, Expected = -0.8153
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6
+R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6
+N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
+D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6
+C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6
+Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6
+E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6
+G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6
+H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6
+I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6
+L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
+K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6
+M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6
+F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6
+P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6
+S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6
+T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6
+W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6
+Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6
+V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6
+B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6
+Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
+X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/src/NAligner/matrices/BLOSUM90 b/src/NAligner/matrices/BLOSUM90
new file mode 100644
index 0000000..71441b5
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUM90
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum90.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 90
+# Entropy = 1.1806, Expected = -0.8887
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -1 -1 -6
+R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 0 -2 -6
+N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
+D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6
+C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6
+Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6
+E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6
+G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6
+H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6
+I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6
+L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
+K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6
+M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6
+F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6
+P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6
+S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -1 -1 -6
+T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -1 -1 -6
+W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -4 -3 -6
+Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6
+V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6
+B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6
+Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
+X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/src/NAligner/matrices/BLOSUMN b/src/NAligner/matrices/BLOSUMN
new file mode 100644
index 0000000..df064c8
--- /dev/null
+++ b/src/NAligner/matrices/BLOSUMN
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosumn.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= -2
+# Entropy = 1.5172, Expected = -1.1484
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -2 -2 -3 -2 -1 -2 -1 -3 -3 -3 -2 -2 -4 -1 1 -1 -4 -4 -1 -3 -2 -1 -7
+R -2 7 -1 -3 -6 0 -2 -4 -1 -5 -4 2 -3 -4 -3 -2 -2 -5 -4 -4 -2 -1 -2 -7
+N -2 -1 7 1 -4 -1 -1 -2 0 -5 -5 -1 -4 -5 -4 0 -1 -6 -4 -4 4 -1 -2 -7
+D -3 -3 1 7 -6 -2 1 -3 -2 -6 -6 -2 -5 -5 -3 -2 -2 -7 -5 -5 4 0 -3 -7
+C -2 -6 -4 -6 9 -5 -7 -5 -6 -2 -3 -5 -3 -3 -5 -2 -2 -5 -4 -2 -5 -6 -4 -7
+Q -1 0 -1 -2 -5 7 1 -4 0 -4 -3 1 -1 -4 -2 -1 -2 -4 -3 -4 -1 4 -2 -7
+E -2 -2 -1 1 -7 1 6 -4 -1 -5 -5 0 -4 -5 -3 -1 -2 -5 -4 -4 0 5 -2 -7
+G -1 -4 -2 -3 -5 -4 -4 6 -4 -6 -6 -3 -5 -5 -4 -1 -3 -5 -6 -5 -2 -4 -3 -7
+H -3 -1 0 -2 -6 0 -1 -4 9 -5 -4 -2 -3 -3 -4 -2 -3 -4 1 -5 -1 -1 -3 -7
+I -3 -5 -5 -6 -2 -4 -5 -6 -5 6 1 -4 1 -1 -5 -4 -2 -4 -3 2 -5 -5 -2 -7
+L -3 -4 -5 -6 -3 -3 -5 -6 -4 1 5 -4 2 0 -5 -4 -3 -4 -3 0 -5 -4 -2 -7
+K -2 2 -1 -2 -5 1 0 -3 -2 -4 -4 6 -2 -4 -2 -1 -2 -6 -4 -4 -1 0 -2 -7
+M -2 -3 -4 -5 -3 -1 -4 -5 -3 1 2 -2 8 -1 -4 -3 -2 -2 -3 0 -5 -3 -2 -7
+F -4 -4 -5 -5 -3 -4 -5 -5 -3 -1 0 -4 -1 7 -5 -4 -3 0 3 -2 -5 -5 -3 -7
+P -1 -3 -4 -3 -5 -2 -3 -4 -4 -5 -5 -2 -4 -5 8 -2 -3 -5 -5 -4 -4 -3 -3 -7
+S 1 -2 0 -2 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 6 1 -4 -3 -3 -1 -1 -1 -7
+T -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -3 -2 -2 -3 -3 1 6 -5 -3 -1 -2 -2 -1 -7
+W -4 -5 -6 -7 -5 -4 -5 -5 -4 -4 -4 -6 -2 0 -5 -4 -5 11 1 -3 -6 -4 -4 -7
+Y -4 -4 -4 -5 -4 -3 -4 -6 1 -3 -3 -4 -3 3 -5 -3 -3 1 8 -3 -4 -4 -3 -7
+V -1 -4 -4 -5 -2 -4 -4 -5 -5 2 0 -4 0 -2 -4 -3 -1 -3 -3 5 -5 -4 -2 -7
+B -3 -2 4 4 -5 -1 0 -2 -1 -5 -5 -1 -5 -5 -4 -1 -2 -6 -4 -5 4 1 -2 -7
+Z -2 -1 -1 0 -6 4 5 -4 -1 -5 -4 0 -3 -5 -3 -1 -2 -4 -4 -4 1 4 -2 -7
+X -1 -2 -2 -3 -4 -2 -2 -3 -3 -2 -2 -2 -2 -3 -3 -1 -1 -4 -3 -2 -2 -2 -2 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/NAligner/matrices/DAYHOFF b/src/NAligner/matrices/DAYHOFF
new file mode 100644
index 0000000..e287ed0
--- /dev/null
+++ b/src/NAligner/matrices/DAYHOFF
@@ -0,0 +1,32 @@
+#Date: Wed, 18 Sep 91 17:36:51 EDT
+#From: altschul at ray.nlm.nih.gov (Stephen Altschul)
+#To: gish at ray.nlm.nih.gov
+#Subject: Vanilla-flavored PAM-250
+#
+# substitution scores for B, Z, X, and * were obtained with "pam" version 1.0.5
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -3 0 0 0 0 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
+G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
+F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
+B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/EDNAFULL b/src/NAligner/matrices/EDNAFULL
new file mode 100644
index 0000000..bfec6d9
--- /dev/null
+++ b/src/NAligner/matrices/EDNAFULL
@@ -0,0 +1,25 @@
+#
+# This matrix was created by Todd Lowe 12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+# nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+ A T G C S W R Y K M B V H D N U
+A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 -4
+T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
+G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 -4
+C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 -4
+S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4
+W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 1
+R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4
+Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 1
+K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 1
+M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4
+B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1
+V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4
+H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1
+D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1
+N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2
+U -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
diff --git a/src/NAligner/matrices/GONNET b/src/NAligner/matrices/GONNET
new file mode 100644
index 0000000..d7bd4f4
--- /dev/null
+++ b/src/NAligner/matrices/GONNET
@@ -0,0 +1,26 @@
+# PAM 250 matrix recommended by Gonnet, Cohen & Benner
+# Science June 5, 1992.
+# Values rounded to nearest integer
+ C S T P A G N D E Q H R K M I L V F Y W X *
+C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8
+S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8
+T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8
+P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8
+A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8
+G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8
+N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8
+D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8
+E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8
+Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8
+H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8
+R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8
+K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8
+M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8
+I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8
+L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8
+V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8
+F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8
+Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8
+W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8
+X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/IDENTITY b/src/NAligner/matrices/IDENTITY
new file mode 100644
index 0000000..63913d5
--- /dev/null
+++ b/src/NAligner/matrices/IDENTITY
@@ -0,0 +1,25 @@
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
+A 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+R -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+N -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+B -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+D -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+C -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+Q -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+Z -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+E -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+G -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+H -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+I -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+L -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+K -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+M -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+F -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+P -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+S -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000
+T -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000
+W -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000
+Y -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000
+V -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000
+X -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 -10000
+* -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0
diff --git a/src/NAligner/matrices/MATCH b/src/NAligner/matrices/MATCH
new file mode 100644
index 0000000..cda9e49
--- /dev/null
+++ b/src/NAligner/matrices/MATCH
@@ -0,0 +1,25 @@
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
+A 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+R -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+N -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+B -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+D -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+C -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+Q -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+Z -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+E -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+G -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1
+P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1
+S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1
+T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1
+W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1
+Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1
+V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
+* -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
diff --git a/src/NAligner/matrices/PAM10 b/src/NAligner/matrices/PAM10
new file mode 100644
index 0000000..c164b06
--- /dev/null
+++ b/src/NAligner/matrices/PAM10
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 10 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -8.27, Entropy = 3.43 bits
+#
+# Lowest score = -23, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 7 -10 -7 -6 -10 -7 -5 -4 -11 -8 -9 -10 -8 -12 -4 -3 -3 -20 -11 -5 -6 -6 -6 -23
+R -10 9 -9 -17 -11 -4 -15 -13 -4 -8 -12 -2 -7 -12 -7 -6 -10 -5 -14 -11 -11 -7 -9 -23
+N -7 -9 9 -1 -17 -7 -5 -6 -2 -8 -10 -4 -15 -12 -9 -2 -5 -11 -7 -12 7 -6 -6 -23
+D -6 -17 -1 8 -21 -6 0 -6 -7 -11 -19 -8 -17 -21 -12 -7 -8 -21 -17 -11 7 -1 -9 -23
+C -10 -11 -17 -21 10 -20 -20 -13 -10 -9 -21 -20 -20 -19 -11 -6 -11 -22 -7 -9 -18 -20 -13 -23
+Q -7 -4 -7 -6 -20 9 -1 -10 -2 -11 -8 -6 -7 -19 -6 -8 -9 -19 -18 -10 -6 7 -8 -23
+E -5 -15 -5 0 -20 -1 8 -7 -9 -8 -13 -7 -10 -20 -9 -7 -9 -23 -11 -10 -1 7 -8 -23
+G -4 -13 -6 -6 -13 -10 -7 7 -13 -17 -14 -10 -12 -12 -10 -4 -10 -21 -20 -9 -6 -8 -8 -23
+H -11 -4 -2 -7 -10 -2 -9 -13 10 -13 -9 -10 -17 -9 -7 -9 -11 -10 -6 -9 -4 -4 -8 -23
+I -8 -8 -8 -11 -9 -11 -8 -17 -13 9 -4 -9 -3 -5 -12 -10 -5 -20 -9 -1 -9 -9 -8 -23
+L -9 -12 -10 -19 -21 -8 -13 -14 -9 -4 7 -11 -2 -5 -10 -12 -10 -9 -10 -5 -12 -10 -9 -23
+K -10 -2 -4 -8 -20 -6 -7 -10 -10 -9 -11 7 -4 -20 -10 -7 -6 -18 -12 -13 -5 -6 -8 -23
+M -8 -7 -15 -17 -20 -7 -10 -12 -17 -3 -2 -4 12 -7 -11 -8 -7 -19 -17 -4 -16 -8 -9 -23
+F -12 -12 -12 -21 -19 -19 -20 -12 -9 -5 -5 -20 -7 9 -13 -9 -12 -7 -1 -12 -14 -20 -12 -23
+P -4 -7 -9 -12 -11 -6 -9 -10 -7 -12 -10 -10 -11 -13 8 -4 -7 -20 -20 -9 -10 -7 -8 -23
+S -3 -6 -2 -7 -6 -8 -7 -4 -9 -10 -12 -7 -8 -9 -4 7 -2 -8 -10 -10 -4 -8 -6 -23
+T -3 -10 -5 -8 -11 -9 -9 -10 -11 -5 -10 -6 -7 -12 -7 -2 8 -19 -9 -6 -6 -9 -7 -23
+W -20 -5 -11 -21 -22 -19 -23 -21 -10 -20 -9 -18 -19 -7 -20 -8 -19 13 -8 -22 -13 -21 -16 -23
+Y -11 -14 -7 -17 -7 -18 -11 -20 -6 -9 -10 -12 -17 -1 -20 -10 -9 -8 10 -10 -9 -13 -11 -23
+V -5 -11 -12 -11 -9 -10 -10 -9 -9 -1 -5 -13 -4 -12 -9 -10 -6 -22 -10 8 -11 -10 -8 -23
+B -6 -11 7 7 -18 -6 -1 -6 -4 -9 -12 -5 -16 -14 -10 -4 -6 -13 -9 -11 7 -3 -8 -23
+Z -6 -7 -6 -1 -20 7 7 -8 -4 -9 -10 -6 -8 -20 -7 -8 -9 -21 -13 -10 -3 7 -8 -23
+X -6 -9 -6 -9 -13 -8 -8 -8 -8 -8 -9 -8 -9 -12 -8 -6 -7 -16 -11 -8 -8 -8 -8 -23
+* -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 1
diff --git a/src/NAligner/matrices/PAM100 b/src/NAligner/matrices/PAM100
new file mode 100644
index 0000000..2e33dd3
--- /dev/null
+++ b/src/NAligner/matrices/PAM100
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 100 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.99, Entropy = 1.18 bits
+#
+# Lowest score = -9, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -3 -1 -1 -3 -2 0 1 -3 -2 -3 -3 -2 -5 1 1 1 -7 -4 0 -1 -1 -1 -9
+R -3 7 -2 -4 -5 1 -3 -5 1 -3 -5 2 -1 -6 -1 -1 -3 1 -6 -4 -3 -1 -2 -9
+N -1 -2 5 3 -5 -1 1 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -3 4 0 -1 -9
+D -1 -4 3 5 -7 0 4 -1 -1 -4 -6 -1 -5 -8 -3 -1 -2 -9 -6 -4 4 3 -2 -9
+C -3 -5 -5 -7 9 -8 -8 -5 -4 -3 -8 -8 -7 -7 -4 -1 -4 -9 -1 -3 -6 -8 -5 -9
+Q -2 1 -1 0 -8 6 2 -3 3 -4 -2 0 -2 -7 -1 -2 -2 -7 -6 -3 0 5 -2 -9
+E 0 -3 1 4 -8 2 5 -1 -1 -3 -5 -1 -4 -8 -2 -1 -2 -9 -5 -3 3 4 -2 -9
+G 1 -5 -1 -1 -5 -3 -1 5 -4 -5 -6 -3 -4 -6 -2 0 -2 -9 -7 -3 -1 -2 -2 -9
+H -3 1 2 -1 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
+I -2 -3 -3 -4 -3 -4 -3 -5 -4 6 1 -3 1 0 -4 -3 0 -7 -3 3 -3 -3 -2 -9
+L -3 -5 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 0 -5 -4 -3 -9
+K -3 2 1 -1 -8 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -6 -6 -4 0 -1 -2 -9
+M -2 -1 -4 -5 -7 -2 -4 -4 -4 1 3 0 9 -1 -4 -3 -1 -6 -5 1 -4 -2 -2 -9
+F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -7 -1 8 -6 -4 -5 -1 4 -3 -6 -7 -4 -9
+P 1 -1 -2 -3 -4 -1 -2 -2 -1 -4 -4 -3 -4 -6 7 0 -1 -7 -7 -3 -3 -1 -2 -9
+S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -3 -4 0 4 2 -3 -4 -2 0 -2 -1 -9
+T 1 -3 0 -2 -4 -2 -2 -2 -3 0 -3 -1 -1 -5 -1 2 5 -7 -4 0 -1 -2 -1 -9
+W -7 1 -5 -9 -9 -7 -9 -9 -4 -7 -3 -6 -6 -1 -7 -3 -7 12 -2 -9 -6 -8 -6 -9
+Y -4 -6 -2 -6 -1 -6 -5 -7 -1 -3 -3 -6 -5 4 -7 -4 -4 -2 9 -4 -4 -6 -4 -9
+V 0 -4 -3 -4 -3 -3 -3 -3 -3 3 0 -4 1 -3 -3 -2 0 -9 -4 5 -4 -3 -2 -9
+B -1 -3 4 4 -6 0 3 -1 1 -3 -5 0 -4 -6 -3 0 -1 -6 -4 -4 4 2 -2 -9
+Z -1 -1 0 3 -8 5 4 -2 1 -3 -4 -1 -2 -7 -1 -2 -2 -8 -6 -3 2 5 -2 -9
+X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM110 b/src/NAligner/matrices/PAM110
new file mode 100644
index 0000000..25b2c01
--- /dev/null
+++ b/src/NAligner/matrices/PAM110
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 110 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.81, Entropy = 1.07 bits
+#
+# Lowest score = -9, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 -1 -1 -3 -1 0 1 -3 -1 -3 -3 -2 -4 1 1 1 -7 -4 0 -1 -1 -1 -9
+R -3 7 -1 -4 -4 1 -3 -4 1 -3 -4 2 -1 -5 -1 -1 -2 1 -5 -4 -2 -1 -2 -9
+N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -5 -2 -3 3 0 -1 -9
+D -1 -4 2 5 -7 1 4 0 0 -3 -6 -1 -5 -7 -3 -1 -1 -8 -5 -4 4 3 -2 -9
+C -3 -4 -5 -7 9 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 -1 -3 -9 -1 -3 -6 -7 -4 -9
+Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -6 -3 0 4 -1 -9
+E 0 -3 1 4 -7 2 5 -1 -1 -3 -5 -1 -3 -7 -2 -1 -2 -9 -5 -3 3 4 -2 -9
+G 1 -4 0 0 -5 -3 -1 5 -4 -4 -6 -3 -4 -5 -2 0 -2 -8 -7 -2 0 -2 -2 -9
+H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
+I -1 -3 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -4 -3 0 -7 -2 3 -3 -3 -2 -9
+L -3 -4 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 1 -5 -3 -2 -9
+K -3 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -5 -5 -4 0 -1 -2 -9
+M -2 -1 -3 -5 -7 -1 -3 -4 -4 1 3 0 8 -1 -4 -2 -1 -6 -5 1 -4 -2 -2 -9
+F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -6 -4 -4 -1 4 -3 -6 -7 -4 -9
+P 1 -1 -2 -3 -4 0 -2 -2 -1 -4 -4 -3 -4 -6 6 0 -1 -7 -7 -2 -2 -1 -2 -9
+S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -2 -4 0 3 2 -3 -3 -2 0 -1 -1 -9
+T 1 -2 0 -1 -3 -2 -2 -2 -3 0 -3 -1 -1 -4 -1 2 5 -6 -3 0 -1 -2 -1 -9
+W -7 1 -5 -8 -9 -6 -9 -8 -4 -7 -3 -5 -6 -1 -7 -3 -6 12 -2 -8 -6 -7 -5 -9
+Y -4 -5 -2 -5 -1 -6 -5 -7 -1 -2 -3 -5 -5 4 -7 -3 -3 -2 8 -4 -3 -5 -3 -9
+V 0 -4 -3 -4 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -4 5 -3 -3 -2 -9
+B -1 -2 3 4 -6 0 3 0 1 -3 -5 0 -4 -6 -2 0 -1 -6 -3 -3 4 2 -1 -9
+Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -7 -1 -1 -2 -7 -5 -3 2 4 -2 -9
+X -1 -2 -1 -2 -4 -1 -2 -2 -2 -2 -2 -2 -2 -4 -2 -1 -1 -5 -3 -2 -1 -2 -2 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM120 b/src/NAligner/matrices/PAM120
new file mode 100644
index 0000000..3cbb04b
--- /dev/null
+++ b/src/NAligner/matrices/PAM120
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.64, Entropy = 0.979 bits
+#
+# Lowest score = -8, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 -8
+R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
+N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 -8
+D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 -8
+C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 -8
+Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 -8
+E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 -8
+G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 -8
+H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 -8
+I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
+L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 -8
+K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 -8
+M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 -8
+F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 -8
+P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 -8
+S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
+T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
+W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 -8
+Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 -8
+V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 -8
+B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 -8
+Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
+X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM130 b/src/NAligner/matrices/PAM130
new file mode 100644
index 0000000..0b47a5d
--- /dev/null
+++ b/src/NAligner/matrices/PAM130
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 130 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.48, Entropy = 0.895 bits
+#
+# Lowest score = -8, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
+R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
+N 0 -1 4 2 -4 0 1 0 2 -2 -3 1 -3 -4 -1 1 0 -4 -2 -3 3 0 -1 -8
+D 0 -3 2 5 -6 1 3 0 0 -3 -5 -1 -4 -7 -2 0 -1 -7 -5 -3 4 3 -1 -8
+C -3 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
+Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -6 0 -1 -2 -6 -5 -3 0 4 -1 -8
+E 0 -3 1 3 -6 2 5 -1 0 -2 -4 -1 -3 -6 -2 -1 -1 -8 -5 -3 2 4 -1 -8
+G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -4 -5 -2 1 -1 -7 -6 -2 0 -1 -2 -8
+H -2 1 2 0 -4 3 0 -3 7 -3 -3 -1 -3 -2 -1 -2 -2 -3 0 -3 1 1 -1 -8
+I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
+L -3 -4 -3 -5 -7 -2 -4 -5 -3 1 5 -4 3 1 -3 -4 -2 -2 -2 1 -4 -3 -2 -8
+K -2 2 1 -1 -6 0 -1 -3 -1 -2 -4 5 0 -6 -2 -1 0 -5 -5 -4 0 0 -1 -8
+M -2 -1 -3 -4 -6 -1 -3 -4 -3 2 3 0 8 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
+F -4 -5 -4 -7 -5 -6 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
+P 1 -1 -1 -2 -3 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -6 -6 -2 -2 -1 -1 -8
+S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
+T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
+W -6 1 -4 -7 -8 -6 -8 -7 -3 -6 -2 -5 -5 -1 -6 -2 -6 12 -1 -7 -5 -7 -5 -8
+Y -4 -5 -2 -5 -1 -5 -5 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -5 -3 -8
+V 0 -3 -3 -3 -2 -3 -3 -2 -3 3 1 -4 1 -2 -2 -2 0 -7 -3 5 -3 -3 -1 -8
+B 0 -2 3 4 -5 0 2 0 1 -3 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
+Z 0 -1 0 3 -6 4 4 -1 1 -3 -3 0 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
+X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 -1 -1 -5 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM140 b/src/NAligner/matrices/PAM140
new file mode 100644
index 0000000..022c61b
--- /dev/null
+++ b/src/NAligner/matrices/PAM140
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 140 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.35, Entropy = 0.820 bits
+#
+# Lowest score = -8, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
+R -2 6 -1 -3 -4 1 -2 -4 1 -2 -4 3 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -1 -8
+N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -8
+D 0 -3 2 4 -6 1 3 0 0 -3 -5 -1 -4 -6 -2 0 -1 -7 -5 -3 4 3 -1 -8
+C -2 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
+Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -2 -5 -5 -2 1 4 -1 -8
+E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -3 -6 -1 -1 -1 -8 -4 -2 2 4 -1 -8
+G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -3 -5 -1 1 -1 -7 -6 -2 0 -1 -1 -8
+H -2 1 2 0 -4 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -8
+I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -2 -2 -1 -8
+L -2 -4 -3 -5 -7 -2 -4 -5 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -8
+K -2 3 1 -1 -6 0 -1 -3 -1 -2 -3 5 0 -6 -2 -1 0 -4 -5 -3 0 0 -1 -8
+M -2 -1 -2 -4 -6 -1 -3 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
+P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -6 -2 -2 -1 -1 -8
+S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 0 -8
+T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -5 -3 0 0 -1 -1 -8
+W -6 1 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 -1 -6 -2 -5 12 -1 -7 -5 -6 -5 -8
+Y -4 -5 -2 -5 -1 -5 -4 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -4 -3 -8
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -2 0 -7 -3 5 -3 -2 -1 -8
+B 0 -2 3 4 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
+Z 0 -1 1 3 -6 4 4 -1 1 -2 -3 0 -2 -6 -1 -1 -1 -6 -4 -2 2 4 -1 -8
+X -1 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -5 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM150 b/src/NAligner/matrices/PAM150
new file mode 100644
index 0000000..c010eef
--- /dev/null
+++ b/src/NAligner/matrices/PAM150
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 150 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.25, Entropy = 0.754 bits
+#
+# Lowest score = -7, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -6 -3 0 0 0 -1 -7
+R -2 6 -1 -2 -4 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -2 1 -4 -3 -2 0 -1 -7
+N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -7
+D 0 -2 2 4 -6 1 3 0 0 -3 -5 -1 -3 -6 -2 0 -1 -7 -4 -3 3 2 -1 -7
+C -2 -4 -4 -6 9 -6 -6 -4 -3 -2 -6 -6 -5 -5 -3 0 -3 -7 0 -2 -5 -6 -3 -7
+Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -7
+E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -2 -6 -1 -1 -1 -7 -4 -2 2 4 -1 -7
+G 1 -3 0 0 -4 -2 -1 4 -3 -3 -4 -2 -3 -5 -1 1 -1 -7 -5 -2 0 -1 -1 -7
+H -2 1 2 0 -3 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -7
+I -1 -2 -2 -3 -2 -3 -2 -3 -3 5 1 -2 2 0 -3 -2 0 -5 -2 3 -2 -2 -1 -7
+L -2 -3 -3 -5 -6 -2 -4 -4 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
+K -2 3 1 -1 -6 0 -1 -2 -1 -2 -3 4 0 -6 -2 -1 0 -4 -4 -3 0 0 -1 -7
+M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -3 1 -3 -2 -1 -7
+F -4 -4 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -3 -1 5 -2 -5 -5 -3 -7
+P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -5 -2 -2 -1 -1 -7
+S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
+T 1 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 4 -5 -3 0 0 -1 -1 -7
+W -6 1 -4 -7 -7 -5 -7 -7 -3 -5 -2 -4 -5 -1 -6 -2 -5 12 -1 -6 -5 -6 -4 -7
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
+B 0 -2 3 3 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -2 3 2 -1 -7
+Z 0 0 1 2 -6 4 4 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 4 -1 -7
+X -1 -1 -1 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -4 -3 -1 -1 -1 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/NAligner/matrices/PAM160 b/src/NAligner/matrices/PAM160
new file mode 100644
index 0000000..f30d717
--- /dev/null
+++ b/src/NAligner/matrices/PAM160
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 160 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.14, Entropy = 0.694 bits
+#
+# Lowest score = -7, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -3 1 1 1 -5 -3 0 0 0 0 -7
+R -2 6 -1 -2 -3 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -1 1 -4 -3 -1 0 -1 -7
+N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -3 -1 1 0 -4 -2 -2 2 1 0 -7
+D 0 -2 2 4 -5 1 3 0 0 -3 -4 0 -3 -6 -2 0 -1 -6 -4 -3 3 2 -1 -7
+C -2 -3 -4 -5 9 -5 -5 -3 -3 -2 -6 -5 -5 -5 -3 0 -2 -7 0 -2 -4 -5 -3 -7
+Q -1 1 0 1 -5 5 2 -2 2 -2 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -7
+E 0 -2 1 3 -5 2 4 0 0 -2 -3 -1 -2 -5 -1 0 -1 -7 -4 -2 2 3 -1 -7
+G 1 -3 0 0 -3 -2 0 4 -3 -3 -4 -2 -3 -4 -1 1 -1 -7 -5 -2 0 -1 -1 -7
+H -2 1 2 0 -3 2 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -2 1 1 -1 -7
+I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 0 -2 -2 0 -5 -2 3 -2 -2 -1 -7
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
+K -2 3 1 0 -5 0 -1 -2 -1 -2 -3 4 0 -5 -2 -1 0 -4 -4 -3 0 0 -1 -7
+M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 0 -2 -2 -1 -4 -3 1 -3 -2 -1 -7
+F -3 -4 -3 -6 -5 -5 -5 -4 -2 0 1 -5 0 7 -4 -3 -3 -1 5 -2 -4 -5 -3 -7
+P 1 -1 -1 -2 -3 0 -1 -1 -1 -2 -3 -2 -2 -4 5 1 0 -5 -5 -2 -1 -1 -1 -7
+S 1 -1 1 0 0 -1 0 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
+T 1 -1 0 -1 -2 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -7
+W -5 1 -4 -6 -7 -5 -7 -7 -3 -5 -2 -4 -4 -1 -5 -2 -5 12 -1 -6 -5 -6 -4 -7
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
+V 0 -3 -2 -3 -2 -2 -2 -2 -2 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
+B 0 -1 2 3 -4 1 2 0 1 -2 -4 0 -3 -4 -1 0 0 -5 -3 -2 3 2 -1 -7
+Z 0 0 1 2 -5 3 3 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 3 -1 -7
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/NAligner/matrices/PAM170 b/src/NAligner/matrices/PAM170
new file mode 100644
index 0000000..ca090d6
--- /dev/null
+++ b/src/NAligner/matrices/PAM170
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 170 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.57, Entropy = 0.640 bits
+#
+# Lowest score = -10, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 0 0 -3 -1 0 1 -3 -1 -3 -2 -2 -5 1 2 2 -8 -5 0 0 0 -1 -10
+R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
+N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -3 -3 3 1 -1 -10
+D 0 -3 3 6 -7 2 5 0 0 -4 -6 -1 -4 -8 -2 0 -1 -9 -6 -4 5 4 -1 -10
+C -3 -5 -5 -7 13 -8 -8 -5 -5 -3 -9 -8 -7 -6 -4 0 -3 -10 0 -3 -6 -8 -4 -10
+Q -1 1 0 2 -8 6 3 -2 4 -3 -2 0 -1 -7 0 -1 -2 -7 -6 -3 1 5 -1 -10
+E 0 -2 2 5 -8 3 6 0 0 -3 -5 -1 -3 -8 -1 -1 -1 -10 -6 -3 3 5 -1 -10
+G 1 -4 0 0 -5 -2 0 6 -4 -4 -6 -3 -4 -6 -2 1 -1 -9 -7 -2 0 -1 -2 -10
+H -3 2 2 0 -5 4 0 -4 9 -4 -3 -1 -4 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
+I -1 -3 -3 -4 -3 -3 -3 -4 -4 7 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
+L -3 -4 -4 -6 -9 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -4 -2 -10
+K -2 4 1 -1 -8 0 -1 -3 -1 -3 -4 6 1 -8 -2 -1 0 -5 -6 -4 0 0 -2 -10
+M -2 -1 -3 -4 -7 -1 -3 -4 -4 2 4 1 10 0 -3 -2 -1 -6 -4 2 -4 -2 -1 -10
+F -5 -6 -5 -8 -6 -7 -8 -6 -3 1 1 -8 0 10 -6 -4 -5 -1 7 -2 -6 -7 -4 -10
+P 1 -1 -1 -2 -4 0 -1 -2 -1 -3 -4 -2 -3 -6 8 1 0 -8 -7 -2 -2 -1 -1 -10
+S 2 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
+T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -5 0 2 5 -7 -4 0 0 -1 -1 -10
+W -8 2 -5 -9 -10 -7 -10 -9 -4 -7 -3 -5 -6 -1 -8 -3 -7 18 -1 -9 -7 -8 -6 -10
+Y -5 -6 -3 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 12 -4 -4 -6 -4 -10
+V 0 -4 -3 -4 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -9 -4 6 -3 -3 -1 -10
+B 0 -2 3 5 -6 1 3 0 1 -3 -5 0 -4 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
+Z 0 0 1 4 -8 5 5 -1 2 -3 -4 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
+X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -2 -1 -4 -1 0 -1 -6 -4 -1 -1 -1 -2 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM180 b/src/NAligner/matrices/PAM180
new file mode 100644
index 0000000..84addeb
--- /dev/null
+++ b/src/NAligner/matrices/PAM180
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 180 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.51, Entropy = 0.591 bits
+#
+# Lowest score = -10, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -8 -5 0 0 0 -1 -10
+R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
+N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -2 -3 3 1 -1 -10
+D 0 -3 3 5 -7 2 4 0 0 -3 -6 0 -4 -8 -2 0 -1 -9 -6 -3 4 3 -1 -10
+C -3 -5 -5 -7 13 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 0 -3 -10 0 -3 -6 -7 -4 -10
+Q -1 1 0 2 -7 6 3 -2 4 -3 -2 0 -1 -6 0 -1 -2 -6 -6 -3 1 5 -1 -10
+E 0 -2 2 4 -7 3 5 0 0 -3 -5 -1 -3 -7 -1 -1 -1 -9 -6 -3 3 5 -1 -10
+G 1 -4 0 0 -5 -2 0 6 -3 -4 -6 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -2 -10
+H -2 2 2 0 -4 4 0 -3 8 -4 -3 -1 -3 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
+I -1 -3 -3 -3 -3 -3 -3 -4 -4 6 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
+L -3 -4 -4 -6 -8 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -3 -2 -10
+K -2 4 1 0 -7 0 -1 -3 -1 -3 -4 6 1 -7 -2 -1 0 -5 -6 -4 0 0 -1 -10
+M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -10
+F -5 -6 -5 -8 -6 -6 -7 -6 -3 1 1 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -10
+P 1 -1 -1 -2 -4 0 -1 -1 -1 -3 -4 -2 -3 -6 8 1 0 -7 -7 -2 -2 -1 -1 -10
+S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
+T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -4 0 2 4 -7 -4 0 0 -1 -1 -10
+W -8 2 -5 -9 -10 -6 -9 -9 -4 -7 -3 -5 -6 0 -7 -3 -7 18 -1 -8 -7 -8 -6 -10
+Y -5 -6 -2 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 11 -4 -4 -6 -3 -10
+V 0 -4 -3 -3 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -8 -4 6 -3 -3 -1 -10
+B 0 -2 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
+Z 0 0 1 3 -7 5 5 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
+X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 0 -1 -6 -3 -1 -1 -1 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM190 b/src/NAligner/matrices/PAM190
new file mode 100644
index 0000000..6840cc4
--- /dev/null
+++ b/src/NAligner/matrices/PAM190
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 190 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.35, Entropy = 0.547 bits
+#
+# Lowest score = -9, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -7 -4 0 0 0 0 -9
+R -2 8 -1 -2 -5 1 -2 -4 2 -3 -4 4 -1 -6 0 -1 -2 2 -5 -3 -1 0 -1 -9
+N 0 -1 3 3 -5 1 2 0 2 -2 -4 1 -3 -4 -1 1 0 -5 -2 -3 3 1 -1 -9
+D 0 -2 3 5 -7 2 4 0 0 -3 -5 0 -4 -7 -2 0 -1 -8 -5 -3 4 3 -1 -9
+C -3 -5 -5 -7 13 -7 -7 -4 -4 -3 -8 -7 -7 -6 -4 0 -3 -9 0 -3 -6 -7 -4 -9
+Q -1 1 1 2 -7 6 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
+E 0 -2 2 4 -7 3 5 0 0 -3 -4 -1 -3 -7 -1 0 -1 -9 -5 -3 3 4 -1 -9
+G 1 -4 0 0 -4 -2 0 6 -3 -4 -5 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -1 -9
+H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
+I -1 -3 -2 -3 -3 -3 -3 -4 -3 6 2 -3 2 1 -3 -2 0 -7 -2 4 -3 -3 -1 -9
+L -3 -4 -4 -5 -8 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -3 -2 2 -5 -3 -2 -9
+K -2 4 1 0 -7 1 -1 -3 -1 -3 -4 6 1 -7 -2 0 0 -5 -6 -3 0 0 -1 -9
+M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -9
+F -5 -6 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -9
+P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
+S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -9
+T 2 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
+W -7 2 -5 -8 -9 -6 -9 -9 -3 -7 -3 -5 -6 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
+Y -4 -5 -2 -5 0 -5 -5 -7 0 -2 -2 -6 -4 7 -6 -4 -3 -1 11 -3 -4 -5 -3 -9
+V 0 -3 -3 -3 -3 -3 -3 -2 -3 4 2 -3 2 -2 -2 -2 0 -8 -3 6 -3 -3 -1 -9
+B 0 -1 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -1 1 0 -6 -4 -3 4 2 -1 -9
+Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -7 -5 -3 2 4 -1 -9
+X 0 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM20 b/src/NAligner/matrices/PAM20
new file mode 100644
index 0000000..58cc98c
--- /dev/null
+++ b/src/NAligner/matrices/PAM20
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 20 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -6.18, Entropy = 2.95 bits
+#
+# Lowest score = -19, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -8 -5 -4 -8 -5 -3 -3 -8 -6 -7 -8 -6 -9 -2 -1 -1 -16 -9 -3 -5 -4 -4 -19
+R -8 9 -7 -12 -9 -2 -11 -11 -3 -6 -10 -1 -5 -10 -5 -4 -8 -3 -11 -9 -9 -5 -7 -19
+N -5 -7 8 1 -13 -5 -3 -4 -1 -6 -8 -2 -11 -10 -7 -1 -3 -9 -5 -9 6 -4 -4 -19
+D -4 -12 1 8 -16 -4 2 -4 -5 -9 -15 -6 -13 -17 -9 -5 -6 -17 -13 -9 6 0 -7 -19
+C -8 -9 -13 -16 10 -16 -16 -11 -8 -7 -17 -16 -16 -15 -9 -4 -9 -18 -5 -7 -14 -16 -11 -19
+Q -5 -2 -5 -4 -16 9 0 -8 0 -9 -6 -4 -5 -15 -4 -6 -7 -15 -14 -8 -4 7 -6 -19
+E -3 -11 -3 2 -16 0 8 -5 -6 -6 -10 -5 -8 -16 -7 -5 -7 -19 -9 -8 0 6 -6 -19
+G -3 -11 -4 -4 -11 -8 -5 7 -10 -13 -12 -8 -10 -10 -7 -3 -7 -17 -16 -7 -4 -6 -6 -19
+H -8 -3 -1 -5 -8 0 -6 -10 9 -11 -7 -8 -13 -7 -5 -7 -8 -8 -4 -7 -2 -2 -6 -19
+I -6 -6 -6 -9 -7 -9 -6 -13 -11 9 -2 -7 -2 -3 -10 -8 -3 -16 -7 1 -7 -7 -6 -19
+L -7 -10 -8 -15 -17 -6 -10 -12 -7 -2 7 -9 0 -4 -8 -9 -8 -7 -8 -3 -10 -8 -7 -19
+K -8 -1 -2 -6 -16 -4 -5 -8 -8 -7 -9 7 -3 -16 -8 -5 -4 -14 -10 -10 -3 -5 -6 -19
+M -6 -5 -11 -13 -16 -5 -8 -10 -13 -2 0 -3 11 -5 -9 -6 -5 -15 -13 -2 -12 -6 -6 -19
+F -9 -10 -10 -17 -15 -15 -16 -10 -7 -3 -4 -16 -5 9 -11 -7 -10 -6 1 -9 -12 -16 -9 -19
+P -2 -5 -7 -9 -9 -4 -7 -7 -5 -10 -8 -8 -9 -11 8 -3 -5 -16 -16 -7 -8 -5 -6 -19
+S -1 -4 -1 -5 -4 -6 -5 -3 -7 -8 -9 -5 -6 -7 -3 7 0 -6 -8 -8 -2 -6 -4 -19
+T -1 -8 -3 -6 -9 -7 -7 -7 -8 -3 -8 -4 -5 -10 -5 0 7 -15 -7 -4 -4 -7 -5 -19
+W -16 -3 -9 -17 -18 -15 -19 -17 -8 -16 -7 -14 -15 -6 -16 -6 -15 13 -6 -18 -11 -17 -13 -19
+Y -9 -11 -5 -13 -5 -14 -9 -16 -4 -7 -8 -10 -13 1 -16 -8 -7 -6 10 -8 -7 -11 -9 -19
+V -3 -9 -9 -9 -7 -8 -8 -7 -7 1 -3 -10 -2 -9 -7 -8 -4 -18 -8 7 -9 -8 -6 -19
+B -5 -9 6 6 -14 -4 0 -4 -2 -7 -10 -3 -12 -12 -8 -2 -4 -11 -7 -9 6 -1 -6 -19
+Z -4 -5 -4 0 -16 7 6 -6 -2 -7 -8 -5 -6 -16 -5 -6 -7 -17 -11 -8 -1 6 -6 -19
+X -4 -7 -4 -7 -11 -6 -6 -6 -6 -6 -7 -6 -6 -9 -6 -4 -5 -13 -9 -6 -6 -6 -6 -19
+* -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 1
diff --git a/src/NAligner/matrices/PAM200 b/src/NAligner/matrices/PAM200
new file mode 100644
index 0000000..d4edff2
--- /dev/null
+++ b/src/NAligner/matrices/PAM200
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 200 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.23, Entropy = 0.507 bits
+#
+# Lowest score = -9, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -3 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -2 -4 1 -2 -4 2 -2 -4 4 -1 -5 0 -1 -1 2 -5 -3 -1 0 -1 -9
+N 0 0 3 3 -5 1 2 0 2 -2 -4 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
+D 0 -2 3 5 -6 2 4 0 0 -3 -5 0 -4 -7 -2 0 0 -8 -5 -3 4 3 -1 -9
+C -3 -4 -5 -6 12 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -9 0 -2 -5 -7 -4 -9
+Q -1 1 1 2 -7 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
+E 0 -2 2 4 -7 3 5 0 0 -3 -4 0 -3 -7 -1 0 -1 -9 -5 -2 3 4 -1 -9
+G 1 -4 0 0 -4 -2 0 6 -3 -3 -5 -2 -4 -6 -1 1 0 -8 -6 -2 0 -1 -1 -9
+H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
+I -1 -2 -2 -3 -3 -3 -3 -3 -3 6 2 -2 2 1 -3 -2 0 -6 -2 4 -3 -3 -1 -9
+L -2 -4 -4 -5 -7 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -2 -2 2 -4 -3 -2 -9
+K -2 4 1 0 -7 1 0 -2 -1 -2 -4 6 1 -7 -2 0 0 -4 -5 -3 0 0 -1 -9
+M -2 -1 -2 -4 -6 -1 -3 -4 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
+F -4 -5 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -6 -3 -9
+P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
+S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 2 2 -3 -3 -1 1 -1 0 -9
+T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
+W -7 2 -5 -8 -9 -6 -9 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
+Y -4 -5 -2 -5 0 -5 -5 -6 0 -2 -2 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
+V 0 -3 -2 -3 -2 -3 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -8 -3 5 -3 -2 -1 -9
+B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -6 -1 1 0 -6 -4 -3 3 2 -1 -9
+Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -6 -1 -1 -1 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM210 b/src/NAligner/matrices/PAM210
new file mode 100644
index 0000000..0b49af5
--- /dev/null
+++ b/src/NAligner/matrices/PAM210
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 210 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.12, Entropy = 0.470 bits
+#
+# Lowest score = -9, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -2 -4 1 -2 -3 2 -2 -4 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -9
+N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
+D 0 -2 2 5 -6 2 4 0 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -9
+C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 0 -2 -5 -6 -4 -9
+Q -1 1 1 2 -6 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -2 1 4 -1 -9
+E 0 -2 2 4 -6 3 5 0 0 -2 -4 0 -3 -6 -1 0 -1 -8 -5 -2 3 4 -1 -9
+G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -9
+H -2 2 2 1 -4 3 0 -3 8 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -9
+I -1 -2 -2 -3 -3 -3 -2 -3 -3 5 2 -2 2 1 -3 -2 0 -6 -1 4 -3 -3 -1 -9
+L -2 -4 -3 -5 -7 -2 -4 -5 -2 2 7 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -9
+K -2 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -2 0 0 -4 -5 -3 0 0 -1 -9
+M -1 -1 -2 -3 -6 -1 -3 -3 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
+F -4 -5 -4 -7 -5 -6 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -9
+P 1 0 -1 -1 -3 0 -1 -1 0 -3 -3 -2 -3 -5 7 1 0 -7 -6 -2 -1 0 -1 -9
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 1 0 0 -9
+T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -9
+W -7 2 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -7 -6 -7 -5 -9
+Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -7 -3 5 -2 -2 -1 -9
+B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
+Z 0 0 1 3 -6 4 4 -1 2 -3 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM220 b/src/NAligner/matrices/PAM220
new file mode 100644
index 0000000..0834a92
--- /dev/null
+++ b/src/NAligner/matrices/PAM220
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 220 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.06, Entropy = 0.437 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
+N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -2 2 4 -6 2 4 0 1 -3 -5 0 -3 -6 -1 0 0 -8 -5 -3 4 3 -1 -8
+C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 0 -2 -5 -6 -3 -8
+Q -1 1 1 2 -6 5 3 -2 3 -2 -2 1 -1 -5 0 -1 -1 -5 -5 -2 1 4 -1 -8
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
+G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -8
+H -2 2 2 1 -4 3 1 -3 7 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -8
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -5 -7 -2 -4 -5 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -1 0 0 -4 -5 -3 0 0 -1 -8
+M -1 -1 -2 -3 -6 -1 -2 -3 -3 2 4 1 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 7 1 0 -6 -6 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 0 0 0 -8
+T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -8
+W -6 2 -4 -8 -8 -5 -8 -8 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -7 -5 -8
+Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 0 11 -3 -3 -5 -3 -8
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -1 -1 0 -7 -3 5 -2 -2 -1 -8
+B 0 -1 2 4 -5 1 3 0 1 -2 -4 0 -3 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM230 b/src/NAligner/matrices/PAM230
new file mode 100644
index 0000000..c9ff6db
--- /dev/null
+++ b/src/NAligner/matrices/PAM230
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 230 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.991, Entropy = 0.407 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -2 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -8
+C -2 -4 -4 -6 12 -6 -6 -4 -4 -2 -7 -6 -6 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
+Q -1 1 1 2 -6 5 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -8
+E 0 -1 1 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
+G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -6 -2 0 -1 -1 -8
+H -2 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -2 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -8
+M -1 -1 -2 -3 -6 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 9 -5 -3 -3 0 7 -1 -5 -6 -3 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -3 1 2 2 -3 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 -1 0 -2 0 -2 0 -1 -3 0 2 3 -6 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -6 -4 -8
+Y -4 -5 -2 -5 0 -4 -5 -6 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -5 -3 -8
+V 0 -3 -2 -2 -2 -2 -2 -2 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -8
+B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -6 -5 -2 2 4 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM240 b/src/NAligner/matrices/PAM240
new file mode 100644
index 0000000..c17cdf8
--- /dev/null
+++ b/src/NAligner/matrices/PAM240
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 240 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.923, Entropy = 0.379 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -5 0 0 -1 2 -4 -3 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+C -2 -4 -4 -5 12 -6 -6 -4 -4 -2 -6 -6 -5 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
+Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
+E 0 -1 1 4 -6 3 4 0 1 -2 -3 0 -2 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
+H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -8
+K -1 3 1 0 -6 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -4 -5 -3 1 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -4 -3 2 -2 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -5 -5 -2 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -3 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -4 -4 0 -6 -3 -5 17 0 -6 -5 -6 -4 -8
+Y -4 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -4 -2 -8
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -6 -3 4 -2 -2 -1 -8
+B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -5 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -6 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM250 b/src/NAligner/matrices/PAM250
new file mode 100644
index 0000000..17e9e60
--- /dev/null
+++ b/src/NAligner/matrices/PAM250
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.844, Entropy = 0.354 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
+G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
+F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
+P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
+B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM260 b/src/NAligner/matrices/PAM260
new file mode 100644
index 0000000..5098eb4
--- /dev/null
+++ b/src/NAligner/matrices/PAM260
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 260 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.794, Entropy = 0.330 bits
+#
+# Lowest score = -7, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -7
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -7
+N 0 0 2 2 -3 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -7
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -5 -1 0 0 -6 -4 -2 3 3 -1 -7
+C -2 -4 -3 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -7 0 -2 -4 -5 -3 -7
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -4 0 0 -1 -5 -4 -2 1 3 0 -7
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 3 3 -1 -7
+G 1 -2 0 1 -3 -1 0 5 -2 -2 -4 -2 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -7
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -7
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -7
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -2 -3 -2 -2 -1 2 -3 -2 -1 -7
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -7
+M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -1 -1 -4 -2 2 -2 -2 -1 -7
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 2 -5 0 9 -4 -3 -3 0 7 -1 -4 -5 -2 -7
+P 1 0 0 -1 -3 0 0 0 0 -2 -2 -1 -2 -4 6 1 0 -5 -5 -1 -1 0 -1 -7
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -2 -3 -1 0 0 0 -7
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 2 -5 -3 0 0 0 0 -7
+W -6 2 -4 -6 -7 -5 -7 -7 -3 -5 -2 -3 -4 0 -5 -2 -5 17 0 -6 -5 -6 -4 -7
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -7
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -7
+B 0 -1 2 3 -4 1 3 1 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 0 -7
+Z 0 0 1 3 -5 3 3 0 2 -2 -2 0 -2 -5 0 0 0 -6 -4 -2 2 3 -1 -7
+X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 0 -1 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/NAligner/matrices/PAM270 b/src/NAligner/matrices/PAM270
new file mode 100644
index 0000000..322fcdb
--- /dev/null
+++ b/src/NAligner/matrices/PAM270
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 270 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.969, Entropy = 0.309 bits
+#
+# Lowest score = -10, Highest score = 23
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 2 -2 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -10
+R -2 8 0 -1 -5 2 -1 -3 2 -2 -4 4 -1 -5 0 0 -1 3 -5 -3 -1 0 -1 -10
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
+D 0 -1 2 5 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -10
+C -2 -5 -4 -6 16 -7 -6 -4 -4 -3 -7 -7 -6 -5 -3 0 -3 -10 1 -2 -5 -7 -4 -10
+Q 0 2 1 2 -7 5 3 -1 4 -2 -2 1 -1 -6 0 -1 -1 -6 -5 -2 2 4 -1 -10
+E 0 -1 2 4 -6 3 5 0 1 -2 -4 0 -3 -7 -1 0 0 -9 -5 -2 3 4 -1 -10
+G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -9 -6 -2 1 0 -1 -10
+H -2 2 2 1 -4 4 1 -2 8 -3 -3 0 -3 -2 0 -1 -1 -3 0 -3 1 2 -1 -10
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 5 -3 -2 -1 -10
+L -2 -4 -3 -5 -7 -2 -4 -5 -3 3 8 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -10
+K -1 4 1 0 -7 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -10
+M -1 -1 -2 -3 -6 -1 -3 -3 -3 3 5 0 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -10
+F -4 -5 -4 -7 -5 -6 -7 -6 -2 1 2 -6 0 12 -6 -4 -4 1 9 -1 -6 -6 -3 -10
+P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -6 7 1 0 -7 -6 -1 -1 0 -1 -10
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -4 -1 1 0 0 -10
+T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -10
+W -7 3 -5 -8 -10 -6 -9 -9 -3 -6 -2 -4 -5 1 -7 -3 -6 23 0 -8 -7 -7 -5 -10
+Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -4 -3 0 13 -3 -4 -5 -3 -10
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 5 2 -3 2 -1 -1 -1 0 -8 -3 5 -2 -2 -1 -10
+B 0 -1 2 4 -5 2 3 1 1 -3 -4 1 -3 -6 -1 1 0 -7 -4 -2 3 3 -1 -10
+Z 0 0 2 3 -7 4 4 0 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 3 4 -1 -10
+X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM280 b/src/NAligner/matrices/PAM280
new file mode 100644
index 0000000..2b09bca
--- /dev/null
+++ b/src/NAligner/matrices/PAM280
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 280 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.916, Entropy = 0.289 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 -1 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
+D 0 -1 2 4 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -2 4 3 -1 -9
+C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -6 -5 -2 2 4 -1 -9
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
+G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 8 -3 -2 0 -2 -2 0 -1 -1 -3 0 -3 1 2 -1 -9
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -5 -7 -2 -4 -5 -2 3 7 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -9
+F -4 -5 -4 -7 -5 -5 -6 -6 -2 1 2 -6 0 11 -5 -4 -4 1 9 -1 -5 -6 -3 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -7 -6 -1 -1 0 -1 -9
+S 1 0 1 0 0 0 0 1 -1 -2 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
+T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 1 1 3 -6 -3 0 0 0 0 -9
+W -7 3 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 22 0 -7 -6 -7 -5 -9
+Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -3 -3 0 13 -3 -4 -5 -3 -9
+V 0 -3 -2 -2 -2 -2 -2 -1 -3 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
+B 0 -1 2 4 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
+Z 0 0 1 3 -6 4 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM290 b/src/NAligner/matrices/PAM290
new file mode 100644
index 0000000..6852c6a
--- /dev/null
+++ b/src/NAligner/matrices/PAM290
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 290 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.877, Entropy = 0.271 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
+D 0 -1 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -8 -5 -2 3 3 -1 -9
+C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -5 -2 2 3 0 -9
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
+G 2 -3 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -9
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
+F -4 -5 -4 -6 -5 -5 -6 -6 -2 1 3 -6 0 11 -5 -4 -3 1 9 -1 -5 -6 -3 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -6 -6 -1 -1 0 -1 -9
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
+T 1 -1 1 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 3 -6 -3 0 0 0 0 -9
+W -7 3 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -7 -5 -9
+Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -2 9 -6 -3 -3 0 13 -3 -4 -5 -2 -9
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
+B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 0 -9
+Z 0 0 1 3 -6 3 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -2 -1 0 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM30 b/src/NAligner/matrices/PAM30
new file mode 100644
index 0000000..8a01c88
--- /dev/null
+++ b/src/NAligner/matrices/PAM30
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -5.06, Entropy = 2.57 bits
+#
+# Lowest score = -17, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
+R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
+N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
+D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
+C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
+Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
+E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
+G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
+H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
+I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
+L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
+K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
+M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
+F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
+P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
+S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
+T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
+W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
+Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
+V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
+B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
+Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
+X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17
+* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
diff --git a/src/NAligner/matrices/PAM300 b/src/NAligner/matrices/PAM300
new file mode 100644
index 0000000..5d1a5a8
--- /dev/null
+++ b/src/NAligner/matrices/PAM300
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 300 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.835, Entropy = 0.254 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 0 -2 0 0 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
+R -1 7 0 -1 -4 2 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -2 -2 2 1 0 -9
+D 0 -1 2 4 -6 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
+C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 -1 -9
+G 2 -2 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -3 -2 -2 -3 -2 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -4 -3 -1 -9
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 3 -6 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 -1 -9
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -6 3 -5 -7 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
+Y -4 -5 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -3 -4 -5 -2 -9
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -3 5 -2 -2 0 -9
+B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
+Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 -1 -9
+X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 -1 0 0 -4 -2 0 0 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM310 b/src/NAligner/matrices/PAM310
new file mode 100644
index 0000000..cd0e5b0
--- /dev/null
+++ b/src/NAligner/matrices/PAM310
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 310 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.779, Entropy = 0.238 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -9
+D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -2 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
+C -2 -4 -4 -5 15 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
+E 0 -1 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -9
+G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 1 -2 -1 0 -5 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -3 -3 -1 -9
+K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -9
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 -1 -9
+F -4 -5 -4 -6 -4 -5 -6 -5 -2 1 3 -5 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -6 3 -4 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
+Y -4 -4 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -2 -4 -4 -2 -9
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
+B 0 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
+Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -9
+X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM320 b/src/NAligner/matrices/PAM320
new file mode 100644
index 0000000..d7fbbd2
--- /dev/null
+++ b/src/NAligner/matrices/PAM320
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 320 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.741, Entropy = 0.224 bits
+#
+# Lowest score = -8, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -8
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -8
+D 1 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -8
+C -2 -4 -4 -5 15 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 0 0 -5 -4 -2 2 3 0 -8
+E 0 -1 2 3 -5 2 4 1 1 -2 -3 0 -2 -5 0 0 0 -7 -5 -2 3 3 0 -8
+G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -8
+H -1 2 2 1 -4 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 0 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -2 -2 0 2 -3 -3 -1 -8
+K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -8
+M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 1 -2 -1 -1 -4 -2 2 -2 -2 0 -8
+F -4 -5 -4 -6 -4 -5 -5 -5 -2 1 3 -5 1 11 -5 -3 -3 1 9 -1 -5 -5 -2 -8
+P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 -1 0 0 -2 0 0 0 -1 0 -2 0 -1 -3 1 1 2 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -6 -6 -4 -8
+Y -4 -4 -2 -5 1 -4 -5 -5 0 -1 0 -5 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
+B 0 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -3 -2 2 2 0 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -8
+X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM330 b/src/NAligner/matrices/PAM330
new file mode 100644
index 0000000..77db35e
--- /dev/null
+++ b/src/NAligner/matrices/PAM330
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 330 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.693, Entropy = 0.210 bits
+#
+# Lowest score = -8, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -4 0 0 -1 3 -4 -2 0 0 -1 -8
+N 0 0 2 2 -4 1 2 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
+D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
+C -2 -4 -4 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
+E 0 -1 2 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 2 3 0 -8
+G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
+H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 4 -2 -2 0 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -3 -1 -2 0 2 -3 -2 -1 -8
+K -1 4 1 0 -5 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 1 -1 -8
+M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -5 -3 -3 1 9 -1 -4 -5 -2 -8
+P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 -1 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
+B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM340 b/src/NAligner/matrices/PAM340
new file mode 100644
index 0000000..02c8540
--- /dev/null
+++ b/src/NAligner/matrices/PAM340
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 340 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.680, Entropy = 0.198 bits
+#
+# Lowest score = -8, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
+R -1 6 0 -1 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 0 -1 -8
+N 0 0 1 2 -3 1 1 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
+D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
+C -2 -4 -3 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
+E 0 0 1 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
+G 1 -2 1 1 -3 -1 1 4 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
+H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 0 -1 -2 0 -2 1 2 0 -8
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 3 -2 -2 0 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -2 -1 -2 0 2 -3 -2 -1 -8
+K -1 4 1 0 -5 1 0 -1 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 1 0 -8
+M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -4 -3 -3 1 9 -1 -4 -5 -2 -8
+P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -4 5 1 1 -5 -5 -1 0 0 0 -8
+S 1 0 1 0 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 0 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 1 -5 -3 -5 22 1 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
+V 0 -2 -1 -2 -2 -2 -1 -1 -2 3 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
+B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM350 b/src/NAligner/matrices/PAM350
new file mode 100644
index 0000000..140a6f2
--- /dev/null
+++ b/src/NAligner/matrices/PAM350
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 350 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.701, Entropy = 0.186 bits
+#
+# Lowest score = -10, Highest score = 27
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 7 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 -1 4 -5 -3 0 1 -1 -10
+N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
+D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -3 -6 0 1 0 -8 -5 -2 3 3 -1 -10
+C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -10 1 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -5 -2 2 3 0 -10
+E 1 0 2 4 -6 3 4 1 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -10
+G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -10
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 5 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 4 8 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -10
+K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -10
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 0 -10
+F -4 -5 -4 -6 -5 -5 -6 -6 -2 2 3 -6 1 13 -5 -4 -3 1 11 -1 -5 -6 -2 -10
+P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -7 -6 -1 0 0 0 -10
+S 1 0 1 1 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 -1 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 27 1 -7 -6 -7 -5 -10
+Y -4 -5 -3 -5 1 -5 -5 -6 0 0 0 -5 -2 11 -6 -3 -3 1 14 -2 -4 -5 -2 -10
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 5 -2 -2 0 -10
+B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -10
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 3 0 -10
+X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -5 -2 0 0 0 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM360 b/src/NAligner/matrices/PAM360
new file mode 100644
index 0000000..5f6cd46
--- /dev/null
+++ b/src/NAligner/matrices/PAM360
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 360 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.697, Entropy = 0.175 bits
+#
+# Lowest score = -9, Highest score = 27
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
+R -1 6 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 -1 -9
+N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -9
+D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -9
+C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 3 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
+E 1 0 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
+G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -7 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -9
+K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 0 -9
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 3 -6 1 12 -5 -4 -3 2 11 -1 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -7 4 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -4 2 -6 -3 -6 27 1 -7 -6 -7 -4 -9
+Y -4 -5 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
+B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -9
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM370 b/src/NAligner/matrices/PAM370
new file mode 100644
index 0000000..f72261f
--- /dev/null
+++ b/src/NAligner/matrices/PAM370
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 370 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.649, Entropy = 0.165 bits
+#
+# Lowest score = -9, Highest score = 27
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 -1 -9
+N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 4 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 18 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
+E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
+G 2 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 1 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -1 -2 0 3 -3 -3 -1 -9
+K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 -1 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -9
+F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 3 -6 1 12 -5 -4 -3 2 11 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -7 3 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 27 1 -7 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -9
+B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 0 -9
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM380 b/src/NAligner/matrices/PAM380
new file mode 100644
index 0000000..cbcf063
--- /dev/null
+++ b/src/NAligner/matrices/PAM380
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 380 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.612, Entropy = 0.156 bits
+#
+# Lowest score = -9, Highest score = 26
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 2 1 2 -5 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 3 3 0 -9
+G 2 -2 1 1 -3 -1 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -1 -2 0 3 -3 -3 -1 -9
+K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -9
+F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 3 -5 1 12 -5 -4 -3 2 10 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -6 3 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 26 1 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -2 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -2 0 -9
+B 1 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM390 b/src/NAligner/matrices/PAM390
new file mode 100644
index 0000000..8206530
--- /dev/null
+++ b/src/NAligner/matrices/PAM390
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 390 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.581, Entropy = 0.147 bits
+#
+# Lowest score = -9, Highest score = 26
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
+R -1 6 1 0 -4 1 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -4 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 3 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -1 2 3 0 -9
+G 1 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -9
+K -1 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 3 -5 1 12 -5 -3 -3 2 10 0 -5 -5 -2 -9
+P 1 0 0 0 -3 0 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
+W -6 3 -4 -7 -9 -5 -7 -7 -3 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -1 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -1 0 -9
+B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM40 b/src/NAligner/matrices/PAM40
new file mode 100644
index 0000000..e0df4f6
--- /dev/null
+++ b/src/NAligner/matrices/PAM40
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -4.27, Entropy = 2.26 bits
+#
+# Lowest score = -15, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2 -3 -2 -3 -15
+R -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7 -6 -3 -5 -15
+N -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7 6 -2 -3 -15
+D -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7 6 2 -5 -15
+C -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5 -11 -12 -8 -15
+Q -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6 -2 6 -4 -15
+E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6 2 6 -4 -15
+G -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5 -2 -4 -4 -15
+H -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6 -1 0 -4 -15
+I -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2 -5 -5 -4 -15
+L -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2 -8 -6 -5 -15
+K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8 -2 -3 -4 -15
+M -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1 -8 -4 -4 -15
+F -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7 -9 -12 -7 -15
+P -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5 -6 -3 -4 -15
+S 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5 -1 -4 -2 -15
+T 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2 -2 -5 -3 -15
+W -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14 -9 -13 -9 -15
+Y -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6 -6 -8 -7 -15
+V -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7 -7 -6 -4 -15
+B -3 -6 6 6 -11 -2 2 -2 -1 -5 -8 -2 -8 -9 -6 -1 -2 -9 -6 -7 6 1 -4 -15
+Z -2 -3 -2 2 -12 6 6 -4 0 -5 -6 -3 -4 -12 -3 -4 -5 -13 -8 -6 1 6 -4 -15
+X -3 -5 -3 -5 -8 -4 -4 -4 -4 -4 -5 -4 -4 -7 -4 -2 -3 -9 -7 -4 -4 -4 -4 -15
+* -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 1
diff --git a/src/NAligner/matrices/PAM400 b/src/NAligner/matrices/PAM400
new file mode 100644
index 0000000..4d99c84
--- /dev/null
+++ b/src/NAligner/matrices/PAM400
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 400 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.521, Entropy = 0.139 bits
+#
+# Lowest score = -8, Highest score = 26
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 1 0 0 -8
+R -1 5 1 0 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 1 0 -8
+N 0 1 1 2 -3 1 2 1 1 -1 -3 1 -1 -3 0 1 0 -4 -3 -1 2 1 0 -8
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -2 2 2 0 -8
+C -2 -4 -3 -5 17 -5 -5 -3 -3 -2 -6 -5 -5 -4 -2 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 2 0 -8
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
+G 1 -2 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -8
+H -1 2 1 1 -3 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -8
+I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -8
+L -2 -3 -3 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -8
+K -1 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -8
+M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 5 1 -1 -1 0 -4 -1 2 -2 -1 0 -8
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 2 3 -5 1 11 -4 -3 -3 2 10 0 -4 -5 -2 -8
+P 1 0 0 0 -2 0 0 0 0 -1 -2 0 -1 -4 5 1 1 -6 -5 -1 0 0 0 -8
+S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -5 -6 -4 -8
+Y -3 -4 -3 -4 1 -4 -4 -5 0 0 0 -4 -1 10 -5 -3 -3 1 13 -2 -3 -4 -2 -8
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -8
+B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 2 0 -8
+Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -8
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/NAligner/matrices/PAM410 b/src/NAligner/matrices/PAM410
new file mode 100644
index 0000000..b7c9bfd
--- /dev/null
+++ b/src/NAligner/matrices/PAM410
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 410 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.617, Entropy = 0.131 bits
+#
+# Lowest score = -10, Highest score = 31
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 1 -5 -3 -1 2 2 0 -10
+D 1 0 2 3 -6 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+C -2 -4 -4 -6 20 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
+E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+G 2 -2 1 1 -4 0 1 5 -1 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 0 -10
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
+L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 8 -3 5 4 -3 -3 -1 -2 1 3 -3 -3 -1 -10
+K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -10
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 14 -5 -4 -3 2 12 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 0 0 -2 -3 0 -2 -5 6 1 1 -7 -5 -1 0 0 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 0 1 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -7 -3 -6 31 2 -7 -6 -7 -4 -10
+Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -2 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
+B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM420 b/src/NAligner/matrices/PAM420
new file mode 100644
index 0000000..53e0caf
--- /dev/null
+++ b/src/NAligner/matrices/PAM420
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 420 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.599, Entropy = 0.124 bits
+#
+# Lowest score = -10, Highest score = 31
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 2 0 -10
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+C -2 -4 -4 -5 20 -6 -6 -3 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
+E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 0 1 1 -8 -6 -1 1 0 0 -10
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
+L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 7 -3 5 4 -2 -3 -1 -2 1 3 -3 -3 -1 -10
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -1 -2 -6 -1 -2 -2 -2 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -10
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -7 -4 -10
+Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
+B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -7 -5 -2 2 3 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM430 b/src/NAligner/matrices/PAM430
new file mode 100644
index 0000000..2450215
--- /dev/null
+++ b/src/NAligner/matrices/PAM430
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 430 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.543, Entropy = 0.117 bits
+#
+# Lowest score = -9, Highest score = 31
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 20 -6 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 3 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -9
+G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -9
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
+F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -7 4 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -9
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -9
+B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -5 -1 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM440 b/src/NAligner/matrices/PAM440
new file mode 100644
index 0000000..0429e87
--- /dev/null
+++ b/src/NAligner/matrices/PAM440
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 440 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.529, Entropy = 0.111 bits
+#
+# Lowest score = -9, Highest score = 30
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -2 2 2 0 -9
+C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
+G 2 -2 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -4 -5 -4 -6 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 30 2 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -4 -2 -9
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -9
+B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM450 b/src/NAligner/matrices/PAM450
new file mode 100644
index 0000000..30cc7a2
--- /dev/null
+++ b/src/NAligner/matrices/PAM450
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 450 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.476, Entropy = 0.105 bits
+#
+# Lowest score = -9, Highest score = 30
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 -1 0 -2 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -4 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -2 0 -2 -9 1 -2 -4 -5 -2 -9
+Q 0 2 1 2 -5 3 2 0 3 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
+G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -2 -3 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -4 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -3 -3 2 12 0 -4 -5 -2 -9
+P 1 0 0 0 -2 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
+W -6 4 -4 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 14 -2 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
+B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM460 b/src/NAligner/matrices/PAM460
new file mode 100644
index 0000000..7491d6c
--- /dev/null
+++ b/src/NAligner/matrices/PAM460
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 460 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.429, Entropy = 0.0994 bits
+#
+# Lowest score = -9, Highest score = 30
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
+R -1 5 1 0 -4 1 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -3 0 1 0 -4 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
+C -2 -4 -3 -5 19 -5 -5 -3 -3 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
+Q 0 1 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 1 2 0 -9
+E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
+G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -7 -5 -1 1 0 0 -9
+H 0 2 1 1 -3 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -1 -2 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -4 -3 -5 -3 -4 -5 -5 -2 2 3 -5 1 12 -4 -3 -3 2 11 0 -4 -5 -2 -9
+P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
+W -6 4 -4 -7 -9 -5 -7 -7 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
+Y -3 -4 -3 -4 2 -4 -4 -5 0 0 1 -4 -1 11 -5 -3 -3 2 14 -2 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
+B 1 0 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 2 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM470 b/src/NAligner/matrices/PAM470
new file mode 100644
index 0000000..9d5e333
--- /dev/null
+++ b/src/NAligner/matrices/PAM470
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 470 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.520, Entropy = 0.0942 bits
+#
+# Lowest score = -10, Highest score = 35
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 1 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 6 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
+N 1 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+C -2 -4 -4 -5 22 -6 -5 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -10 2 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -10
+G 2 -1 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 1 1 1 -8 -6 -1 1 1 0 -10
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 8 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -1 -2 -6 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -4 -3 -1 1 0 0 -10
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -4 -6 35 2 -7 -6 -7 -4 -10
+Y -4 -5 -3 -5 2 -4 -5 -6 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -10
+B 1 0 2 3 -5 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
+Z 0 1 1 3 -6 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -7 -5 -1 2 3 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM480 b/src/NAligner/matrices/PAM480
new file mode 100644
index 0000000..c777c62
--- /dev/null
+++ b/src/NAligner/matrices/PAM480
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 480 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.494, Entropy = 0.0893 bits
+#
+# Lowest score = -10, Highest score = 35
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 1 1 -2 0 1 2 0 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -10
+N 1 1 1 2 -4 1 2 1 1 -1 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -1 2 2 0 -10
+C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -10 2 -2 -4 -5 -3 -10
+Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -8 -5 -1 2 3 0 -10
+G 2 -1 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -10
+H 0 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
+I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
+L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
+F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
+W -7 4 -5 -7 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -3 -6 35 2 -7 -6 -6 -4 -10
+Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 3 -1 -1 0 -10
+B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
+Z 0 1 1 2 -5 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -6 -5 -1 2 2 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/PAM490 b/src/NAligner/matrices/PAM490
new file mode 100644
index 0000000..107a0c8
--- /dev/null
+++ b/src/NAligner/matrices/PAM490
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 490 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.431, Entropy = 0.0847 bits
+#
+# Lowest score = -9, Highest score = 34
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 0 0 -1 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 2 -2 -4 -5 -2 -9
+Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+G 2 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
+H 0 2 1 1 -4 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -1 -3 -2 -3 -6 -2 -3 -3 -2 4 7 -2 5 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 4 1 1 -6 -5 -1 0 1 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -2 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
+B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM50 b/src/NAligner/matrices/PAM50
new file mode 100644
index 0000000..6d37d4b
--- /dev/null
+++ b/src/NAligner/matrices/PAM50
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 50 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -3.70, Entropy = 2.00 bits
+#
+# Lowest score = -13, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -5 -2 -2 -5 -3 -1 -1 -5 -3 -5 -5 -4 -7 0 0 0 -11 -6 -1 -2 -2 -2 -13
+R -5 8 -4 -7 -6 0 -7 -7 0 -4 -7 1 -3 -8 -3 -2 -5 -1 -8 -6 -5 -2 -4 -13
+N -2 -4 7 2 -8 -2 -1 -2 1 -4 -6 0 -6 -7 -4 1 -1 -7 -3 -6 5 -1 -2 -13
+D -2 -7 2 7 -11 -1 3 -2 -2 -6 -10 -3 -8 -12 -6 -2 -3 -12 -9 -6 6 2 -4 -13
+C -5 -6 -8 -11 9 -11 -11 -7 -6 -5 -12 -11 -11 -10 -6 -2 -6 -13 -3 -5 -9 -11 -7 -13
+Q -3 0 -2 -1 -11 8 2 -5 2 -6 -4 -2 -3 -10 -2 -4 -4 -10 -9 -5 -2 6 -3 -13
+E -1 -7 -1 3 -11 2 7 -3 -3 -4 -7 -3 -5 -11 -4 -3 -4 -13 -7 -5 2 6 -3 -13
+G -1 -7 -2 -2 -7 -5 -3 6 -7 -8 -9 -6 -7 -8 -4 -1 -4 -12 -11 -4 -2 -4 -4 -13
+H -5 0 1 -2 -6 2 -3 -7 9 -7 -5 -4 -8 -5 -3 -4 -5 -6 -2 -5 0 0 -4 -13
+I -3 -4 -4 -6 -5 -6 -4 -8 -7 8 0 -5 0 -1 -7 -5 -1 -11 -5 3 -5 -5 -3 -13
+L -5 -7 -6 -10 -12 -4 -7 -9 -5 0 6 -6 2 -1 -6 -7 -5 -5 -5 -1 -7 -5 -5 -13
+K -5 1 0 -3 -11 -2 -3 -6 -4 -5 -6 6 -1 -11 -5 -3 -2 -9 -8 -7 -1 -2 -4 -13
+M -4 -3 -6 -8 -11 -3 -5 -7 -8 0 2 -1 10 -3 -6 -4 -3 -10 -8 0 -7 -4 -4 -13
+F -7 -8 -7 -12 -10 -10 -11 -8 -5 -1 -1 -11 -3 9 -8 -5 -7 -3 3 -6 -9 -11 -6 -13
+P 0 -3 -4 -6 -6 -2 -4 -4 -3 -7 -6 -5 -6 -8 8 -1 -3 -11 -11 -4 -5 -3 -4 -13
+S 0 -2 1 -2 -2 -4 -3 -1 -4 -5 -7 -3 -4 -5 -1 6 1 -4 -5 -4 -1 -3 -2 -13
+T 0 -5 -1 -3 -6 -4 -4 -4 -5 -1 -5 -2 -3 -7 -3 1 6 -10 -5 -2 -2 -4 -2 -13
+W -11 -1 -7 -12 -13 -10 -13 -12 -6 -11 -5 -9 -10 -3 -11 -4 -10 13 -4 -12 -8 -11 -9 -13
+Y -6 -8 -3 -9 -3 -9 -7 -11 -2 -5 -5 -8 -8 3 -11 -5 -5 -4 9 -6 -5 -8 -6 -13
+V -1 -6 -6 -6 -5 -5 -5 -4 -5 3 -1 -7 0 -6 -4 -4 -2 -12 -6 7 -6 -5 -3 -13
+B -2 -5 5 6 -9 -2 2 -2 0 -5 -7 -1 -7 -9 -5 -1 -2 -8 -5 -6 5 1 -3 -13
+Z -2 -2 -1 2 -11 6 6 -4 0 -5 -5 -2 -4 -11 -3 -3 -4 -11 -8 -5 1 6 -3 -13
+X -2 -4 -2 -4 -7 -3 -3 -4 -4 -3 -5 -4 -4 -6 -4 -2 -2 -9 -6 -3 -3 -3 -4 -13
+* -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 1
diff --git a/src/NAligner/matrices/PAM500 b/src/NAligner/matrices/PAM500
new file mode 100644
index 0000000..617c3f1
--- /dev/null
+++ b/src/NAligner/matrices/PAM500
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 500 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.401, Entropy = 0.0803 bits
+#
+# Lowest score = -9, Highest score = 34
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+C -2 -4 -3 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
+Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -1 -5 0 1 0 -7 -5 -1 2 2 0 -9
+G 1 -1 1 1 -3 0 1 4 -1 -2 -3 0 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
+H 0 2 1 1 -4 2 1 -1 4 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -1 -2 -2 -3 -6 -2 -3 -3 -2 4 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 0 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -1 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -1 -1 0 -9
+F -3 -4 -4 -5 -3 -4 -5 -5 -2 2 4 -5 1 13 -4 -3 -3 3 13 0 -4 -5 -2 -9
+P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 1 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -6 4 -5 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
+Y -3 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -1 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -1 3 -1 -1 0 -9
+B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -1 -4 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/NAligner/matrices/PAM60 b/src/NAligner/matrices/PAM60
new file mode 100644
index 0000000..fba70b9
--- /dev/null
+++ b/src/NAligner/matrices/PAM60
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 60 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -3.21, Entropy = 1.79 bits
+#
+# Lowest score = -12, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -5 -2 -2 -5 -3 -1 0 -5 -3 -4 -5 -3 -6 0 1 1 -10 -6 -1 -2 -2 -2 -12
+R -5 8 -3 -6 -6 0 -6 -7 0 -4 -6 2 -2 -7 -2 -2 -4 0 -8 -5 -5 -2 -4 -12
+N -2 -3 6 2 -7 -2 0 -1 1 -4 -5 0 -6 -6 -4 1 -1 -6 -3 -5 5 -1 -2 -12
+D -2 -6 2 7 -10 -1 3 -2 -2 -5 -9 -2 -7 -11 -5 -2 -3 -11 -8 -6 5 2 -3 -12
+C -5 -6 -7 -10 9 -10 -10 -7 -6 -4 -11 -10 -10 -9 -6 -1 -5 -12 -2 -4 -9 -10 -6 -12
+Q -3 0 -2 -1 -10 7 2 -5 2 -5 -3 -1 -2 -9 -1 -3 -4 -9 -8 -5 -1 6 -3 -12
+E -1 -6 0 3 -10 2 7 -2 -3 -4 -7 -3 -5 -10 -3 -2 -4 -12 -7 -4 2 5 -3 -12
+G 0 -7 -1 -2 -7 -5 -2 6 -6 -7 -8 -5 -6 -7 -4 0 -3 -11 -10 -4 -2 -3 -3 -12
+H -5 0 1 -2 -6 2 -3 -6 8 -6 -4 -4 -7 -4 -2 -4 -5 -5 -2 -5 0 0 -3 -12
+I -3 -4 -4 -5 -4 -5 -4 -7 -6 7 0 -4 1 -1 -6 -4 -1 -10 -4 3 -4 -4 -3 -12
+L -4 -6 -5 -9 -11 -3 -7 -8 -4 0 6 -6 2 -1 -5 -6 -5 -4 -5 -1 -7 -5 -4 -12
+K -5 2 0 -2 -10 -1 -3 -5 -4 -4 -6 6 0 -10 -4 -2 -2 -8 -7 -6 -1 -2 -3 -12
+M -3 -2 -6 -7 -10 -2 -5 -6 -7 1 2 0 10 -2 -6 -4 -2 -9 -7 0 -6 -4 -3 -12
+F -6 -7 -6 -11 -9 -9 -10 -7 -4 -1 -1 -10 -2 8 -7 -5 -6 -3 3 -5 -8 -10 -5 -12
+P 0 -2 -4 -5 -6 -1 -3 -4 -2 -6 -5 -4 -6 -7 7 0 -2 -10 -10 -4 -4 -2 -3 -12
+S 1 -2 1 -2 -1 -3 -2 0 -4 -4 -6 -2 -4 -5 0 5 1 -4 -5 -4 0 -3 -2 -12
+T 1 -4 -1 -3 -5 -4 -4 -3 -5 -1 -5 -2 -2 -6 -2 1 6 -9 -5 -1 -2 -4 -2 -12
+W -10 0 -6 -11 -12 -9 -12 -11 -5 -10 -4 -8 -9 -3 -10 -4 -9 13 -3 -11 -8 -11 -8 -12
+Y -6 -8 -3 -8 -2 -8 -7 -10 -2 -4 -5 -7 -7 3 -10 -5 -5 -3 9 -5 -5 -7 -5 -12
+V -1 -5 -5 -6 -4 -5 -4 -4 -5 3 -1 -6 0 -5 -4 -4 -1 -11 -5 6 -5 -5 -3 -12
+B -2 -5 5 5 -9 -1 2 -2 0 -4 -7 -1 -6 -8 -4 0 -2 -8 -5 -5 5 1 -3 -12
+Z -2 -2 -1 2 -10 6 5 -3 0 -4 -5 -2 -4 -10 -2 -3 -4 -11 -7 -5 1 5 -3 -12
+X -2 -4 -2 -3 -6 -3 -3 -3 -3 -3 -4 -3 -3 -5 -3 -2 -2 -8 -5 -3 -3 -3 -3 -12
+* -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 1
diff --git a/src/NAligner/matrices/PAM70 b/src/NAligner/matrices/PAM70
new file mode 100644
index 0000000..b20cdf0
--- /dev/null
+++ b/src/NAligner/matrices/PAM70
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.77, Entropy = 1.60 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -1 -2 -11
+R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -2 -3 -11
+N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -1 -2 -11
+D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 2 -3 -11
+C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -9 -6 -11
+Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 5 -2 -11
+E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -3 -11
+G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -3 -3 -11
+H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 1 -3 -11
+I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 -4 -3 -11
+L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 -4 -4 -11
+K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -2 -3 -11
+M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 -3 -3 -11
+F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -9 -5 -11
+P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -2 -3 -11
+S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -2 -1 -11
+T 1 -4 0 -2 -5 -3 -3 -3 -4 -1 -4 -1 -2 -6 -2 2 6 -8 -4 -1 -1 -3 -2 -11
+W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -10 -7 -11
+Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -7 -5 -11
+V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 -4 -2 -11
+B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 1 -2 -11
+Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 5 -3 -11
+X -2 -3 -2 -3 -6 -2 -3 -3 -3 -3 -4 -3 -3 -5 -3 -1 -2 -7 -5 -2 -2 -3 -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
diff --git a/src/NAligner/matrices/PAM80 b/src/NAligner/matrices/PAM80
new file mode 100644
index 0000000..55aa043
--- /dev/null
+++ b/src/NAligner/matrices/PAM80
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.55, Entropy = 1.44 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -4 -1 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -5 0 1 1 -8 -5 0 -1 -1 -1 -11
+R -4 7 -2 -5 -5 0 -4 -6 0 -3 -5 2 -2 -6 -2 -1 -3 0 -7 -5 -3 -1 -3 -11
+N -1 -2 5 3 -6 -1 0 -1 2 -3 -5 0 -4 -5 -3 1 0 -5 -3 -4 4 0 -1 -11
+D -1 -5 3 6 -9 0 4 -1 -1 -4 -7 -2 -6 -9 -4 -1 -2 -10 -7 -5 5 2 -3 -11
+C -4 -5 -6 -9 9 -9 -9 -6 -5 -4 -9 -9 -8 -8 -5 -1 -4 -10 -2 -3 -7 -9 -5 -11
+Q -2 0 -1 0 -9 7 2 -4 2 -4 -3 -1 -2 -8 -1 -3 -3 -8 -7 -4 0 5 -2 -11
+E -1 -4 0 4 -9 2 6 -2 -2 -3 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -2 -11
+G 0 -6 -1 -1 -6 -4 -2 6 -5 -6 -7 -4 -5 -6 -3 0 -2 -10 -8 -3 -1 -2 -3 -11
+H -4 0 2 -1 -5 2 -2 -5 8 -5 -4 -3 -5 -3 -2 -3 -4 -4 -1 -4 0 1 -2 -11
+I -2 -3 -3 -4 -4 -4 -3 -6 -5 7 1 -4 1 0 -5 -4 -1 -8 -3 3 -4 -4 -2 -11
+L -4 -5 -5 -7 -9 -3 -6 -7 -4 1 6 -5 2 0 -4 -5 -4 -3 -4 0 -6 -4 -3 -11
+K -4 2 0 -2 -9 -1 -2 -4 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -6 -5 -1 -1 -3 -11
+M -3 -2 -4 -6 -8 -2 -4 -5 -5 1 2 0 9 -2 -5 -3 -2 -7 -6 1 -5 -3 -2 -11
+F -5 -6 -5 -9 -8 -8 -9 -6 -3 0 0 -9 -2 8 -7 -4 -5 -2 4 -4 -7 -8 -5 -11
+P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -4 -4 -5 -7 7 0 -2 -9 -8 -3 -3 -2 -2 -11
+S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -5 -2 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -11
+T 1 -3 0 -2 -4 -3 -3 -2 -4 -1 -4 -1 -2 -5 -2 2 5 -8 -4 -1 -1 -3 -1 -11
+W -8 0 -5 -10 -10 -8 -11 -10 -4 -8 -3 -7 -7 -2 -9 -3 -8 13 -2 -10 -7 -9 -7 -11
+Y -5 -7 -3 -7 -2 -7 -6 -8 -1 -3 -4 -6 -6 4 -8 -4 -4 -2 9 -5 -4 -6 -4 -11
+V 0 -5 -4 -5 -3 -4 -4 -3 -4 3 0 -5 1 -4 -3 -3 -1 -10 -5 6 -4 -4 -2 -11
+B -1 -3 4 5 -7 0 2 -1 0 -4 -6 -1 -5 -7 -3 0 -1 -7 -4 -4 5 2 -2 -11
+Z -1 -1 0 2 -9 5 5 -2 1 -4 -4 -1 -3 -8 -2 -2 -3 -9 -6 -4 2 5 -2 -11
+X -1 -3 -1 -3 -5 -2 -2 -3 -2 -2 -3 -3 -2 -5 -2 -1 -1 -7 -4 -2 -2 -2 -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
diff --git a/src/NAligner/matrices/PAM90 b/src/NAligner/matrices/PAM90
new file mode 100644
index 0000000..fa2d5b3
--- /dev/null
+++ b/src/NAligner/matrices/PAM90
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 90 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.26, Entropy = 1.30 bits
+#
+# Lowest score = -10, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -4 -1 -1 -3 -2 0 0 -4 -2 -3 -3 -2 -5 0 1 1 -8 -5 0 -1 -1 -1 -10
+R -4 7 -2 -5 -5 0 -4 -5 1 -3 -5 2 -2 -6 -1 -1 -3 0 -6 -4 -3 -1 -2 -10
+N -1 -2 5 3 -6 -1 0 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -4 4 0 -1 -10
+D -1 -5 3 6 -8 0 4 -1 -1 -4 -7 -2 -5 -8 -4 -1 -2 -9 -6 -4 5 3 -2 -10
+C -3 -5 -6 -8 9 -8 -8 -5 -5 -3 -9 -8 -8 -7 -5 -1 -4 -10 -1 -3 -7 -8 -5 -10
+Q -2 0 -1 0 -8 6 2 -3 2 -4 -3 -1 -2 -7 -1 -2 -3 -7 -6 -4 0 5 -2 -10
+E 0 -4 0 4 -8 2 6 -1 -1 -3 -5 -2 -4 -8 -2 -2 -2 -10 -6 -3 2 5 -2 -10
+G 0 -5 -1 -1 -5 -3 -1 5 -5 -5 -6 -4 -5 -6 -3 0 -2 -9 -8 -3 -1 -2 -2 -10
+H -4 1 2 -1 -5 2 -1 -5 8 -5 -3 -2 -5 -3 -2 -3 -3 -4 -1 -4 1 1 -2 -10
+I -2 -3 -3 -4 -3 -4 -3 -5 -5 6 1 -3 1 0 -4 -3 0 -8 -3 3 -3 -3 -2 -10
+L -3 -5 -4 -7 -9 -3 -5 -6 -3 1 6 -5 2 0 -4 -5 -3 -3 -3 0 -5 -4 -3 -10
+K -3 2 1 -2 -8 -1 -2 -4 -2 -3 -5 5 0 -8 -3 -1 -1 -6 -6 -5 0 -1 -2 -10
+M -2 -2 -4 -5 -8 -2 -4 -5 -5 1 2 0 9 -1 -4 -3 -2 -7 -6 1 -5 -3 -2 -10
+F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -8 -1 8 -6 -4 -5 -2 4 -4 -6 -8 -4 -10
+P 0 -1 -2 -4 -5 -1 -2 -3 -2 -4 -4 -3 -4 -6 7 0 -1 -8 -8 -3 -3 -2 -2 -10
+S 1 -1 1 -1 -1 -2 -2 0 -3 -3 -5 -1 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -10
+T 1 -3 0 -2 -4 -3 -2 -2 -3 0 -3 -1 -2 -5 -1 2 5 -7 -4 -1 -1 -2 -1 -10
+W -8 0 -5 -9 -10 -7 -10 -9 -4 -8 -3 -6 -7 -2 -8 -3 -7 13 -2 -9 -7 -8 -6 -10
+Y -5 -6 -2 -6 -1 -6 -6 -8 -1 -3 -3 -6 -6 4 -8 -4 -4 -2 9 -4 -4 -6 -4 -10
+V 0 -4 -4 -4 -3 -4 -3 -3 -4 3 0 -5 1 -4 -3 -3 -1 -9 -4 6 -4 -3 -2 -10
+B -1 -3 4 5 -7 0 2 -1 1 -3 -5 0 -5 -6 -3 0 -1 -7 -4 -4 4 2 -2 -10
+Z -1 -1 0 3 -8 5 5 -2 1 -3 -4 -1 -3 -8 -2 -2 -2 -8 -6 -3 2 5 -2 -10
+X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/NAligner/matrices/TEST1 b/src/NAligner/matrices/TEST1
new file mode 100644
index 0000000..8b5954e
--- /dev/null
+++ b/src/NAligner/matrices/TEST1
@@ -0,0 +1,25 @@
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
+A 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+R -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+N -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+B -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+D -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+C -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+Q -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+Z -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+E -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+G -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1
+F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1 -1
+P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1 -1
+S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1 -1
+T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1 -1
+W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1 -1
+Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1 -1
+V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 5 -1 -1
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
+* -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
diff --git a/src/NAligner/naligner.sln b/src/NAligner/naligner.sln
new file mode 100644
index 0000000..6a226c2
--- /dev/null
+++ b/src/NAligner/naligner.sln
@@ -0,0 +1,21 @@
+Microsoft Visual Studio Solution File, Format Version 8.00
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "naligner", "naligner.csproj", "{68BB6B9B-57B5-4E16-8B23-952CD406CE9B}"
+ ProjectSection(ProjectDependencies) = postProject
+ EndProjectSection
+EndProject
+Global
+ GlobalSection(SolutionConfiguration) = preSolution
+ Debug = Debug
+ Release = Release
+ EndGlobalSection
+ GlobalSection(ProjectConfiguration) = postSolution
+ {68BB6B9B-57B5-4E16-8B23-952CD406CE9B}.Debug.ActiveCfg = Debug|.NET
+ {68BB6B9B-57B5-4E16-8B23-952CD406CE9B}.Debug.Build.0 = Debug|.NET
+ {68BB6B9B-57B5-4E16-8B23-952CD406CE9B}.Release.ActiveCfg = Release|.NET
+ {68BB6B9B-57B5-4E16-8B23-952CD406CE9B}.Release.Build.0 = Release|.NET
+ EndGlobalSection
+ GlobalSection(ExtensibilityGlobals) = postSolution
+ EndGlobalSection
+ GlobalSection(ExtensibilityAddIns) = postSolution
+ EndGlobalSection
+EndGlobal
diff --git a/src/NAligner/util/AlphanumericComparator.cs b/src/NAligner/util/AlphanumericComparator.cs
new file mode 100644
index 0000000..fdc7ab7
--- /dev/null
+++ b/src/NAligner/util/AlphanumericComparator.cs
@@ -0,0 +1,71 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System.Collections;
+
+namespace NAligner.util
+{
+ /// <summary> Comparator to sort the scoring matrices by their names. </summary>
+ public class AlphanumericComparator : IComparer
+ {
+ public virtual int Compare(object o1, object o2)
+ {
+ string s1 = (string) o1;
+ string s2 = (string) o2;
+
+ int index1 = FirstDigitIndex(s1);
+ int index2 = FirstDigitIndex(s2);
+
+ if (index1 == - 1 || index2 == - 1)
+ {
+ return string.Compare(s1, s2, true);
+ }
+ else
+ {
+ string s3 = s1.Substring(0, (index1) - (0));
+ string s4 = s2.Substring(0, (index2) - (0));
+ if (s3.ToUpper().Equals(s4.ToUpper()))
+ {
+ return System.Int32.Parse(s1.Substring(index1)).CompareTo(
+ System.Int32.Parse(s2.Substring(index2)));
+ }
+ else
+ {
+ return string.Compare(s1, s2, true);
+ }
+ }
+ }
+
+ /// <summary> Returns the index of the first digit in a String.
+ /// If there are no digits, returns -1.</summary>
+ private int FirstDigitIndex(string s)
+ {
+ for (int i = 0; i < s.Length; i++)
+ {
+ if (s[i] >= '0' && s[i] <= '9')
+ {
+ return i;
+ }
+ }
+ return - 1;
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/util/Commons.cs b/src/NAligner/util/Commons.cs
new file mode 100644
index 0000000..f17d67f
--- /dev/null
+++ b/src/NAligner/util/Commons.cs
@@ -0,0 +1,115 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System;
+
+namespace NAligner.util
+{
+ /// <summary> Global constants and varilables </summary>
+ public abstract class Commons
+ {
+ /// <summary> Returns system file separator.</summary>
+ /// <returns> file separator </returns>
+ public static string FileSeparator
+ {
+ get { return fileSeparator; }
+
+ }
+
+ /// <summary> Returns system line separator.</summary>
+ /// <returns> line separator </returns>
+ public static string LineSeparator
+ {
+ get { return lineSeparator; }
+
+ }
+
+ /// <summary> Returns user's current directory.</summary>
+ /// <returns> user's current directory </returns>
+ public static string UserDirectory
+ {
+ get { return userDirectory; }
+
+ }
+
+ /// <summary> Returns the current release version of JAligner</summary>
+ public static string CurrentRelease
+ {
+ get { return CURRENT_RELEASE; }
+
+ }
+
+ /// <summary> Current release version of JAligner</summary>
+ private const string CURRENT_RELEASE = "0.9";
+
+ /// <summary> Default home directory</summary>
+ private const string DEFAULT_USER_DIRECTORY = ".";
+
+ /// <summary> Default file separator</summary>
+ private const string DEFAULT_FILE_SEPARATOR = "/";
+
+ /// <summary> Default line separator</summary>
+ private const string DEFAULT_LINE_SEPARATOR = "\r\n";
+
+ /// <summary> User home directory</summary>
+ private static string userDirectory = DEFAULT_USER_DIRECTORY;
+
+ /// <summary> Line separator</summary>
+ private static string fileSeparator = DEFAULT_FILE_SEPARATOR;
+
+ /// <summary> Line separator</summary>
+ private static string lineSeparator = DEFAULT_LINE_SEPARATOR;
+
+ static Commons()
+ {
+ {
+ try
+ {
+ userDirectory = System.Environment.CurrentDirectory;
+ }
+ catch (System.Exception e)
+ {
+ Console.Error.WriteLine("Failed getting user current directory: " + e.ToString());
+ }
+ }
+ {
+ try
+ {
+ fileSeparator = System.IO.Path.DirectorySeparatorChar.ToString();
+ }
+ catch (System.Exception e)
+ {
+ System.Console.Error.WriteLine("Failed getting system file separator: " + e.ToString());
+ }
+ }
+ {
+ try
+ {
+ lineSeparator = System.Environment.NewLine;
+ }
+ catch (System.Exception e)
+ {
+ System.Console.Error.WriteLine("Failed getting system line separator: " + e.ToString());
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/util/NAlignerException.cs b/src/NAligner/util/NAlignerException.cs
new file mode 100644
index 0000000..d74c9d0
--- /dev/null
+++ b/src/NAligner/util/NAlignerException.cs
@@ -0,0 +1,38 @@
+#region NAligner Copyright
+/*
+ * NAligner
+ * C# port of JAligner API, http://jaligner.sourceforge.net
+ *
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+*/
+#endregion
+
+using System;
+
+namespace NAligner.util
+{
+ /// <summary> JAligner exception </summary>
+ [Serializable]
+ public class NAlignerException : Exception
+ {
+ public NAlignerException() : base() {}
+
+ public NAlignerException(string message) : base(message) {}
+
+ public NAlignerException(string message, Exception cause) : base(message, cause) {}
+
+ public NAlignerException(Exception cause) : base("", cause) {}
+ }
+}
\ No newline at end of file
diff --git a/src/NAligner/util/Tokenizer.cs b/src/NAligner/util/Tokenizer.cs
new file mode 100644
index 0000000..63a1181
--- /dev/null
+++ b/src/NAligner/util/Tokenizer.cs
@@ -0,0 +1,195 @@
+using System;
+using System.Collections;
+
+namespace NAligner.util
+{
+ /// <summary>The class performs token processing in strings</summary>
+ /// <remarks>Class create by the Java Language Conversion Assistant.</remarks>
+ public class Tokenizer : IEnumerator
+ {
+ /// Position over the string
+ private long currentPos = 0;
+
+ /// Include demiliters in the results.
+ private bool includeDelims = false;
+
+ /// Char representation of the String to tokenize.
+ private char[] chars = null;
+
+ //The tokenizer uses the default delimiter set: the space character, the tab character, the newline character, and the carriage-return character and the form-feed character
+ private string delimiters = " \t\n\r\f";
+
+ /// <summary>
+ /// Initializes a new class instance with a specified string to process
+ /// </summary>
+ /// <param name="source">String to tokenize</param>
+ public Tokenizer(string source)
+ {
+ this.chars = source.ToCharArray();
+ }
+
+ /// <summary>
+ /// Initializes a new class instance with a specified string to process
+ /// and the specified token delimiters to use
+ /// </summary>
+ /// <param name="source">String to tokenize</param>
+ /// <param name="delimiters">String containing the delimiters</param>
+ public Tokenizer(string source, string delimiters) : this(source)
+ {
+ this.delimiters = delimiters;
+ }
+
+
+ /// <summary>
+ /// Initializes a new class instance with a specified string to process, the specified token
+ /// delimiters to use, and whether the delimiters must be included in the results.
+ /// </summary>
+ /// <param name="source">String to tokenize</param>
+ /// <param name="delimiters">String containing the delimiters</param>
+ /// <param name="includeDelims">Determines if delimiters are included in the results.</param>
+ public Tokenizer(string source, string delimiters, bool includeDelims) : this(source, delimiters)
+ {
+ this.includeDelims = includeDelims;
+ }
+
+
+ /// <summary>
+ /// Returns the next token from the token list
+ /// </summary>
+ /// <returns>The string value of the token</returns>
+ public string NextToken()
+ {
+ return NextToken(this.delimiters);
+ }
+
+ /// <summary>
+ /// Returns the next token from the source string, using the provided
+ /// token delimiters
+ /// </summary>
+ /// <param name="delimiters">String containing the delimiters to use</param>
+ /// <returns>The string value of the token</returns>
+ public string NextToken(string delimiters)
+ {
+ //According to documentation, the usage of the received delimiters should be temporary (only for this call).
+ //However, it seems it is not true, so the following line is necessary.
+ this.delimiters = delimiters;
+
+ //at the end
+ if (this.currentPos == this.chars.Length)
+ throw new System.ArgumentOutOfRangeException();
+ //if over a delimiter and delimiters must be returned
+ else if ((System.Array.IndexOf(delimiters.ToCharArray(), chars[this.currentPos]) != -1)
+ && this.includeDelims)
+ return "" + this.chars[this.currentPos++];
+ //need to get the token wo delimiters.
+ else
+ return nextToken(delimiters.ToCharArray());
+ }
+
+ //Returns the nextToken wo delimiters
+ private string nextToken(char[] delimiters)
+ {
+ string token = "";
+ long pos = this.currentPos;
+
+ //skip possible delimiters
+ while (System.Array.IndexOf(delimiters, this.chars[currentPos]) != -1)
+ //The last one is a delimiter (i.e there is no more tokens)
+ if (++this.currentPos == this.chars.Length)
+ {
+ this.currentPos = pos;
+ throw new System.ArgumentOutOfRangeException();
+ }
+
+ //getting the token
+ while (System.Array.IndexOf(delimiters, this.chars[this.currentPos]) == -1)
+ {
+ token += this.chars[this.currentPos];
+ //the last one is not a delimiter
+ if (++this.currentPos == this.chars.Length)
+ break;
+ }
+ return token;
+ }
+
+
+ /// <summary>
+ /// Determines if there are more tokens to return from the source string
+ /// </summary>
+ /// <returns>True or false, depending if there are more tokens</returns>
+ public bool HasMoreTokens()
+ {
+ //keeping the current pos
+ long pos = this.currentPos;
+
+ try
+ {
+ this.NextToken();
+ }
+ catch (System.ArgumentOutOfRangeException)
+ {
+ return false;
+ }
+ finally
+ {
+ this.currentPos = pos;
+ }
+ return true;
+ }
+
+ /// <summary>
+ /// Remaining tokens count
+ /// </summary>
+ public int Count
+ {
+ get
+ {
+ //keeping the current pos
+ long pos = this.currentPos;
+ int i = 0;
+
+ try
+ {
+ while (true)
+ {
+ this.NextToken();
+ i++;
+ }
+ }
+ catch (System.ArgumentOutOfRangeException)
+ {
+ this.currentPos = pos;
+ return i;
+ }
+ }
+ }
+
+ /// <summary>
+ /// Performs the same action as NextToken.
+ /// </summary>
+ public System.Object Current
+ {
+ get { return (Object) this.NextToken(); }
+ }
+
+ /// <summary>
+ /// Performs the same action as HasMoreTokens.
+ /// </summary>
+ /// <returns>True or false, depending if there are more tokens</returns>
+ public bool MoveNext()
+ {
+ return this.HasMoreTokens();
+ }
+
+ /// <summary>
+ /// Does nothing.
+ /// </summary>
+ public void Reset()
+ {
+ ;
+ }
+ }
+
+
+
+}
\ No newline at end of file
diff --git a/src/jaligner/Alignment.java b/src/jaligner/Alignment.java
new file mode 100644
index 0000000..7592331
--- /dev/null
+++ b/src/jaligner/Alignment.java
@@ -0,0 +1,442 @@
+/*
+ * $Id: Alignment.java,v 1.19 2005/04/02 17:10:27 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner;
+
+import jaligner.matrix.Matrix;
+import jaligner.util.Commons;
+
+import java.text.DecimalFormat;
+
+/**
+ * Holds the output of a pairwise sequences alignment.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class Alignment {
+
+ /**
+ * Gap character
+ */
+ public static final char GAP = '-';
+
+ /**
+ * Default name for sequence #1
+ */
+ private static final String DEFAULT_SEQUENCE1_NAME = "jaligner_1";
+
+ /**
+ * Default name for sequence #2
+ */
+ private static final String DEFAULT_SEQUENCE2_NAME = "jaligner_2";
+
+ /**
+ * Scoring matrix
+ */
+ private Matrix matrix;
+
+ /**
+ * Gap open cost
+ */
+ private float open;
+
+ /**
+ * Gap extend cost
+ */
+ private float extend;
+
+ /**
+ * Alignment score
+ */
+ private float score;
+
+ /**
+ * Aligned sequence #1
+ */
+ private char[] sequence1;
+
+ /**
+ * Name of sequence #1
+ */
+ private String name1;
+
+ /**
+ * Alignment start location in sequence #1
+ */
+ private int start1;
+
+ /**
+ * Aligned sequence #2
+ */
+ private char[] sequence2;
+
+ /**
+ * Name of sequence #2
+ */
+ private String name2;
+
+ /**
+ * Alignment start location in sequence #2
+ */
+ private int start2;
+
+ /**
+ * Markup line
+ */
+ private char[] markupLine;
+
+ /**
+ * Count of identical locations
+ */
+ private int identity;
+
+ /**
+ * Count of similar locations
+ */
+ private int similarity;
+
+ /**
+ * Count of gap locations
+ */
+ private int gaps;
+
+ /**
+ * Constructor for Alignment
+ */
+
+ public Alignment() {
+ super();
+ }
+
+ /**
+ * @return Returns the extend.
+ */
+ public float getExtend() {
+ return extend;
+ }
+
+ /**
+ * @param extend
+ * The extend to set.
+ */
+ public void setExtend(float extend) {
+ this.extend = extend;
+ }
+
+ /**
+ * @return Returns the matrix.
+ */
+ public Matrix getMatrix() {
+ return matrix;
+ }
+
+ /**
+ * @param matrix
+ * The matrix to set.
+ */
+ public void setMatrix(Matrix matrix) {
+ this.matrix = matrix;
+ }
+
+ /**
+ * @return Returns the name1.
+ */
+ public String getName1() {
+ return name1 == null || name1.length() == 0 ? DEFAULT_SEQUENCE1_NAME
+ : name1;
+ }
+
+ /**
+ * @param name1
+ * The name1 to set.
+ */
+ public void setName1(String name1) {
+ this.name1 = name1;
+ }
+
+ /**
+ * @return Returns the name2.
+ */
+ public String getName2() {
+ return name2 == null || name2.length() == 0 ? DEFAULT_SEQUENCE2_NAME
+ : name2;
+ }
+
+ /**
+ * @param name2
+ * The name2 to set.
+ */
+ public void setName2(String name2) {
+ this.name2 = name2;
+ }
+
+ /**
+ * @return Returns the open.
+ */
+ public float getOpen() {
+ return open;
+ }
+
+ /**
+ * @param open
+ * The open to set.
+ */
+ public void setOpen(float open) {
+ this.open = open;
+ }
+
+ /**
+ * @return Returns the score.
+ */
+ public float getScore() {
+ return score;
+ }
+
+ /**
+ * @param score
+ * The score to set.
+ */
+ public void setScore(float score) {
+ this.score = score;
+ }
+
+ /**
+ * @return Returns the sequence1.
+ */
+ public char[] getSequence1() {
+ return sequence1;
+ }
+
+ /**
+ * @param sequence1
+ * The sequence1 to set.
+ */
+ public void setSequence1(char[] sequence1) {
+ this.sequence1 = sequence1;
+ }
+
+ /**
+ * @return Returns the sequence2.
+ */
+ public char[] getSequence2() {
+ return sequence2;
+ }
+
+ /**
+ * @param sequence2
+ * The sequence2 to set.
+ */
+ public void setSequence2(char[] sequence2) {
+ this.sequence2 = sequence2;
+ }
+
+ /**
+ * @return Returns the start1.
+ */
+ public int getStart1() {
+ return start1;
+ }
+
+ /**
+ * @param start1
+ * The start1 to set.
+ */
+ public void setStart1(int start1) {
+ this.start1 = start1;
+ }
+
+ /**
+ * @return Returns the start2.
+ */
+ public int getStart2() {
+ return start2;
+ }
+
+ /**
+ * @param start2
+ * The start2 to set.
+ */
+ public void setStart2(int start2) {
+ this.start2 = start2;
+ }
+
+ /**
+ * @return Returns the gaps.
+ */
+ public int getGaps() {
+ return gaps;
+ }
+
+ /**
+ * @param gaps
+ * The gaps to set.
+ */
+ public void setGaps(int gaps) {
+ this.gaps = gaps;
+ }
+
+ /**
+ * @return Returns the identity.
+ */
+ public int getIdentity() {
+ return identity;
+ }
+
+ /**
+ * @param identity
+ * The identity to set.
+ */
+ public void setIdentity(int identity) {
+ this.identity = identity;
+ }
+
+ /**
+ * @return Returns the markupLine.
+ */
+ public char[] getMarkupLine() {
+ return markupLine;
+ }
+
+ /**
+ * @param markupLine
+ * The markupLine to set.
+ */
+ public void setMarkupLine(char[] markupLine) {
+ this.markupLine = markupLine;
+ }
+
+ /**
+ * @return Returns the similarity.
+ */
+ public int getSimilarity() {
+ return similarity;
+ }
+
+ /**
+ * @param similarity
+ * The similarity to set.
+ */
+ public void setSimilarity(int similarity) {
+ this.similarity = similarity;
+ }
+
+ /**
+ * Returns a summary for alignment
+ *
+ * @return alignment summary
+ */
+ public String getSummary() {
+ StringBuffer buffer = new StringBuffer();
+ DecimalFormat f1 = new DecimalFormat("0.00");
+ DecimalFormat f2 = new DecimalFormat("0.00%");
+
+ int length = getSequence1().length;
+
+ buffer.append("Sequence #1: " + getName1());
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Sequence #2: " + getName2());
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Length #1: " + sequence1.length);
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Length #2: " + sequence2.length);
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Matrix: "
+ + (matrix.getId() == null ? "" : matrix.getId()));
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Gap open: " + open);
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Gap extend: " + extend);
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Length: " + length);
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Identity: " + identity + "/" + length + " ("
+ + f2.format(identity / (float) length) + ")");
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Similarity: " + similarity + "/" + length + " ("
+ + f2.format(similarity / (float) length) + ")");
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Gaps: " + gaps + "/" + length + " ("
+ + f2.format(gaps / (float) length) + ")");
+ buffer.append(Commons.getLineSeparator());
+ buffer.append("Score: " + f1.format(score));
+ buffer.append(Commons.getLineSeparator());
+
+ return buffer.toString();
+ }
+
+ /**
+ * Calculate the score of the alignment, not using the score field (the
+ * function only uses sequence1, sequence2, matrix and gap penalties). (By:
+ * Bram Minnaert)
+ *
+ * @return the calculated score
+ */
+ public float calculateScore() {
+ float calcScore = 0; // the calculated score
+ boolean previous1wasGap = false; // in the previous step there was a gap
+ // in the first sequence
+ boolean previous2wasGap = false; // in the previous step there was a gap
+ // in the second sequence
+ char c1, c2; // the next character
+ for (int i = 0, n = sequence1.length; i < n; i++) {
+ c1 = sequence1[i];
+ c2 = sequence2[i];
+ // the next character in the first sequence is a gap
+ if (c1 == GAP) {
+ if (previous1wasGap) {
+ calcScore -= extend;
+ } else {
+ calcScore -= open;
+ }
+ previous1wasGap = true;
+ previous2wasGap = false;
+ }
+ // the next character in the second sequence is a gap
+ else if (c2 == GAP) {
+ if (previous2wasGap) {
+ calcScore -= extend;
+ } else {
+ calcScore -= open;
+ }
+ previous1wasGap = false;
+ previous2wasGap = true;
+ }
+ // the next characters in boths sequences are not gaps
+ else {
+ calcScore += matrix.getScore(c1, c2);
+ previous1wasGap = false;
+ previous2wasGap = false;
+ }
+ }
+ return calcScore;
+ }
+
+ /**
+ * Check if the calculated score matches the field score.
+ *
+ * @return true if equal, else false. (By: Bram Minnaert)
+ */
+ public boolean checkScore() {
+ if (calculateScore() == score) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/Cell.java b/src/jaligner/Cell.java
new file mode 100644
index 0000000..e452403
--- /dev/null
+++ b/src/jaligner/Cell.java
@@ -0,0 +1,98 @@
+/*
+ * $Id: Cell.java,v 1.5 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner;
+
+/**
+ * A cell in a similarity matrix, to hold row, column and score.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class Cell {
+ /**
+ * Row of the cell
+ */
+ private int row;
+ /**
+ * Column of the cell
+ */
+ private int col;
+ /**
+ * Alignment score at this cell
+ */
+ private float score;
+
+ /**
+ * Constructor
+ */
+ public Cell() {
+ super();
+ this.row = 0;
+ this.col = 0;
+ this.score = Float.NEGATIVE_INFINITY;
+ }
+ /**
+ * @return Returns the col.
+ */
+ public int getCol() {
+ return this.col;
+ }
+ /**
+ * @param col The col to set.
+ */
+ public void setCol(int col) {
+ this.col = col;
+ }
+ /**
+ * @return Returns the row.
+ */
+ public int getRow() {
+ return this.row;
+ }
+ /**
+ * @param row The row to set.
+ */
+ public void setRow(int row) {
+ this.row = row;
+ }
+ /**
+ * @return Returns the score.
+ */
+ public float getScore() {
+ return this.score;
+ }
+ /**
+ * @param score The score to set.
+ */
+ public void setScore(float score) {
+ this.score = score;
+ }
+
+ /**
+ * Sets the row, column and score of the cell.
+ * @param row The row to set.
+ * @param col The col to set.
+ * @param score The score to set.
+ */
+ public void set(int row, int col, float score) {
+ this.row = row;
+ this.col = col;
+ this.score = score;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/Directions.java b/src/jaligner/Directions.java
new file mode 100644
index 0000000..f876864
--- /dev/null
+++ b/src/jaligner/Directions.java
@@ -0,0 +1,44 @@
+/*
+ * $Id: Directions.java,v 1.10 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner;
+
+/**
+ * Traceback directions.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public abstract class Directions {
+ /**
+ * Traceback direction stop
+ */
+ public static final byte STOP = 0;
+ /**
+ * Traceback direction left
+ */
+ public static final byte LEFT = 1;
+ /**
+ * Traceback direction diagonal
+ */
+ public static final byte DIAGONAL = 2;
+ /**
+ * Traceback direction up
+ */
+ public static final byte UP = 3;
+}
\ No newline at end of file
diff --git a/src/jaligner/Markups.java b/src/jaligner/Markups.java
new file mode 100644
index 0000000..4b3b342
--- /dev/null
+++ b/src/jaligner/Markups.java
@@ -0,0 +1,47 @@
+/*
+ * $Id: Markups.java,v 1.2 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner;
+
+/**
+ * Markups line characters.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public abstract class Markups {
+ /**
+ * Markup line identity character
+ */
+ public static final char IDENTITY = '|';
+
+ /**
+ * Markup line similarity character
+ */
+ public static final char SIMILARITY = ':';
+
+ /**
+ * Markup line gap character
+ */
+ public static final char GAP = ' ';
+
+ /**
+ * Markup line mismatch character
+ */
+ public static final char MISMATCH = '.';
+}
diff --git a/src/jaligner/Sequence.java b/src/jaligner/Sequence.java
new file mode 100644
index 0000000..2d6e823
--- /dev/null
+++ b/src/jaligner/Sequence.java
@@ -0,0 +1,195 @@
+/*
+ * $Id: Sequence.java,v 1.12 2005/04/14 14:44:45 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner;
+
+import java.io.Serializable;
+
+/**
+ * A basic (nucleic or protein) sequence. It's a wrapper to {@link java.lang.String}.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class Sequence implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3256721801357898297L;
+
+ /**
+ * Sequence type nucleic.
+ */
+ public static final int NUCLEIC = 0;
+
+ /**
+ * Sequence type protein.
+ */
+ public static final int PROTEIN = 1;
+
+ /**
+ * Sequence
+ */
+ private String sequence;
+
+ /**
+ * Sequence id.
+ */
+ private String id = null;
+
+ /**
+ * Sequence description.
+ */
+ private String description = null;
+
+ /**
+ * Sequence type.
+ */
+ private int type = PROTEIN;
+
+ /**
+ * Constructor
+ */
+ public Sequence( ) {
+ super();
+ }
+
+ /**
+ * Constructor
+ * @param sequence
+ */
+ public Sequence(String sequence) {
+ super();
+ this.sequence = sequence;
+ }
+
+
+ /**
+ * Constructor
+ * @param sequence
+ * @param id
+ * @param description
+ * @param type
+ */
+ public Sequence(String sequence, String id, String description, int type) {
+ super();
+ this.sequence = sequence;
+ this.id = id;
+ this.description = description;
+ this.type = type;
+ }
+
+ /**
+ * Returns the sequence string
+ * @return Returns the sequence
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the sequence string
+ * @param sequence The sequence to set
+ */
+ public void setSequence(String sequence) {
+ this.sequence = sequence;
+ }
+
+ /**
+ * Returns the sequence id
+ * @return Returns the id
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the sequence id
+ * @param id The id to set
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ /**
+ * Returns the sequence description
+ * @return Returns the description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the sequence description
+ * @param description The description to set
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * Returns the sequence type (nucleic or protein)
+ * @return Returns the type
+ */
+ public int getType() {
+ return type;
+ }
+
+ /**
+ * Sets the sequence type (nucleic or protein)
+ * @param type The type to set
+ */
+ public void setType(int type) {
+ this.type = type;
+ }
+
+ /**
+ * Returns the length of the sequence
+ * @return sequence length
+ */
+ public int length( ) {
+ return this.sequence.length();
+ }
+
+ /**
+ * Returns a subsequence
+ * @param index start index
+ * @param length length of subsequence
+ * @return subsequence
+ */
+ public String subsequence(int index, int length) {
+ return this.sequence.substring(index, index + length);
+ }
+
+ /**
+ * Returns the acid at specific location in the sequence
+ * @param index
+ * @return acid at index
+ */
+ public char acidAt(int index) {
+ return this.sequence.charAt(index);
+ }
+
+ /**
+ * Returns the sequence as an array of characters.
+ * @return array of chars.
+ */
+ public char[] toArray( ) {
+ return this.sequence.toCharArray();
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/SmithWatermanGotoh.java b/src/jaligner/SmithWatermanGotoh.java
new file mode 100644
index 0000000..7e48bdb
--- /dev/null
+++ b/src/jaligner/SmithWatermanGotoh.java
@@ -0,0 +1,358 @@
+/*
+ * $Id: SmithWatermanGotoh.java,v 1.18 2005/04/03 19:38:21 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner;
+
+import jaligner.matrix.Matrix;
+
+import java.util.logging.Logger;
+
+/**
+ * An implementation of the Smith-Waterman algorithm with Gotoh's improvement
+ * for biological local pairwise sequence alignment.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class SmithWatermanGotoh {
+ /**
+ * Hidden constructor
+ */
+ private SmithWatermanGotoh() {
+ super();
+ }
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger
+ .getLogger(SmithWatermanGotoh.class.getName());
+
+ /**
+ * Aligns two sequences by Smith-Waterman algorithm
+ *
+ * @param s1
+ * sequene #1 ({@link Sequence})
+ * @param s2
+ * sequene #2 ({@link Sequence})
+ * @param matrix
+ * scoring matrix ({@link Matrix})
+ * @param o
+ * open gap penalty
+ * @param e
+ * extend gap penalty
+ * @return alignment object contains the two aligned sequences, the
+ * alignment score and alignment statistics
+ * @see Sequence
+ * @see Matrix
+ */
+ public static Alignment align(Sequence s1, Sequence s2, Matrix matrix,
+ float o, float e) {
+ logger.info("Started...");
+ long start = System.currentTimeMillis();
+ float[][] scores = matrix.getScores();
+
+ SmithWatermanGotoh sw = new SmithWatermanGotoh();
+
+ int m = s1.length() + 1;
+ int n = s2.length() + 1;
+
+ byte[] pointers = new byte[m * n];
+
+ // Initializes the boundaries of the traceback matrix to STOP.
+ for (int i = 0, k = 0; i < m; i++, k += n) {
+ pointers[k] = Directions.STOP;
+ }
+ for (int j = 1; j < n; j++) {
+ pointers[j] = Directions.STOP;
+ }
+
+ short[] sizesOfVerticalGaps = new short[m * n];
+ short[] sizesOfHorizontalGaps = new short[m * n];
+ for (int i = 0, k = 0; i < m; i++, k += n) {
+ for (int j = 0; j < n; j++) {
+ sizesOfVerticalGaps[k + j] = sizesOfHorizontalGaps[k + j] = 1;
+ }
+ }
+
+ Cell cell = sw.construct(s1, s2, scores, o, e, pointers,
+ sizesOfVerticalGaps, sizesOfHorizontalGaps);
+ Alignment alignment = sw.traceback(s1, s2, matrix, pointers, cell,
+ sizesOfVerticalGaps, sizesOfHorizontalGaps);
+ alignment.setName1(s1.getId());
+ alignment.setName2(s2.getId());
+ alignment.setMatrix(matrix);
+ alignment.setOpen(o);
+ alignment.setExtend(e);
+ logger.info("Finished in " + (System.currentTimeMillis() - start)
+ + " milliseconds");
+ return alignment;
+ }
+
+ /**
+ * Constructs directions matrix for the traceback
+ *
+ * @param s1
+ * sequence #1
+ * @param s2
+ * sequence #2
+ * @param matrix
+ * scoring matrix
+ * @param o
+ * open gap penalty
+ * @param e
+ * extend gap penalty
+ * @return The cell where the traceback starts.
+ */
+ private Cell construct(Sequence s1, Sequence s2, float[][] matrix, float o,
+ float e, byte[] pointers, short[] sizesOfVerticalGaps,
+ short[] sizesOfHorizontalGaps) {
+ logger.info("Started...");
+ long start = System.currentTimeMillis();
+
+ char[] a1 = s1.toArray();
+ char[] a2 = s2.toArray();
+
+ int m = s1.length() + 1;
+ int n = s2.length() + 1;
+
+ float f; // score of alignment x1...xi to y1...yi if xi aligns to yi
+ float[] g = new float[n]; // score if xi aligns to a gap after yi
+ float h; // score if yi aligns to a gap after xi
+ float[] v = new float[n]; // best score of alignment x1...xi to y1...yi
+ float vDiagonal;
+
+ g[0] = Float.NEGATIVE_INFINITY;
+ h = Float.NEGATIVE_INFINITY;
+ v[0] = 0;
+
+ for (int j = 1; j < n; j++) {
+ g[j] = Float.NEGATIVE_INFINITY;
+ v[j] = 0;
+ }
+
+ float similarityScore, g1, g2, h1, h2;
+
+ Cell cell = new Cell();
+
+ for (int i = 1, k = n; i < m; i++, k += n) {
+ h = Float.NEGATIVE_INFINITY;
+ vDiagonal = v[0];
+ for (int j = 1, l = k + 1; j < n; j++, l++) {
+ similarityScore = matrix[a1[i - 1]][a2[j - 1]];
+
+ // Fill the matrices
+ f = vDiagonal + similarityScore;
+
+ g1 = g[j] - e;
+ g2 = v[j] - o;
+ if (g1 > g2) {
+ g[j] = g1;
+ sizesOfVerticalGaps[l] = (short) (sizesOfVerticalGaps[l - n] + 1);
+ } else {
+ g[j] = g2;
+ }
+
+ h1 = h - e;
+ h2 = v[j - 1] - o;
+ if (h1 > h2) {
+ h = h1;
+ sizesOfHorizontalGaps[l] = (short) (sizesOfHorizontalGaps[l - 1] + 1);
+ } else {
+ h = h2;
+ }
+
+ vDiagonal = v[j];
+ v[j] = maximum(f, g[j], h, 0);
+
+ // Determine the traceback direction
+ if (v[j] == 0) {
+ pointers[l] = Directions.STOP;
+ } else if (v[j] == f) {
+ pointers[l] = Directions.DIAGONAL;
+ } else if (v[j] == g[j]) {
+ pointers[l] = Directions.UP;
+ } else {
+ pointers[l] = Directions.LEFT;
+ }
+
+ // Set the traceback start at the current cell i, j and score
+ if (v[j] > cell.getScore()) {
+ cell.set(i, j, v[j]);
+ }
+ }
+ }
+ logger.info("Finished in " + (System.currentTimeMillis() - start)
+ + " milliseconds");
+ return cell;
+ }
+
+ /**
+ * Returns the alignment of two sequences based on the passed array of
+ * pointers
+ *
+ * @param s1
+ * sequence #1
+ * @param s2
+ * sequence #2
+ * @param m
+ * scoring matrix
+ * @param cell
+ * The cell where the traceback starts.
+ * @return {@link Alignment}with the two aligned sequences and alignment
+ * score.
+ * @see Cell
+ * @see Alignment
+ */
+ private Alignment traceback(Sequence s1, Sequence s2, Matrix m,
+ byte[] pointers, Cell cell, short[] sizesOfVerticalGaps,
+ short[] sizesOfHorizontalGaps) {
+ logger.info("Started...");
+ long start = System.currentTimeMillis();
+
+ char[] a1 = s1.toArray();
+ char[] a2 = s2.toArray();
+
+ float[][] scores = m.getScores();
+
+ int n = s2.length() + 1;
+
+ Alignment alignment = new Alignment();
+ alignment.setScore(cell.getScore());
+
+ int maxlen = s1.length() + s2.length(); // maximum length after the
+ // aligned sequences
+
+ char[] reversed1 = new char[maxlen]; // reversed sequence #1
+ char[] reversed2 = new char[maxlen]; // reversed sequence #2
+ char[] reversed3 = new char[maxlen]; // reversed markup
+
+ int len1 = 0; // length of sequence #1 after alignment
+ int len2 = 0; // length of sequence #2 after alignment
+ int len3 = 0; // length of the markup line
+
+ int identity = 0; // count of identitcal pairs
+ int similarity = 0; // count of similar pairs
+ int gaps = 0; // count of gaps
+
+ char c1, c2;
+
+ int i = cell.getRow(); // traceback start row
+ int j = cell.getCol(); // traceback start col
+ int k = i * n;
+
+ boolean stillGoing = true; // traceback flag: true -> continue & false
+ // -> stop
+
+ while (stillGoing) {
+ switch (pointers[k + j]) {
+ case Directions.UP:
+ for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++) {
+ reversed1[len1++] = a1[--i];
+ reversed2[len2++] = Alignment.GAP;
+ reversed3[len3++] = Markups.GAP;
+ k -= n;
+ gaps++;
+ }
+ break;
+ case Directions.DIAGONAL:
+ c1 = a1[--i];
+ c2 = a2[--j];
+ k -= n;
+ reversed1[len1++] = c1;
+ reversed2[len2++] = c2;
+ if (c1 == c2) {
+ reversed3[len3++] = Markups.IDENTITY;
+ identity++;
+ similarity++;
+ } else if (scores[c1][c2] > 0) {
+ reversed3[len3++] = Markups.SIMILARITY;
+ similarity++;
+ } else {
+ reversed3[len3++] = Markups.MISMATCH;
+ }
+ break;
+ case Directions.LEFT:
+ for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++) {
+ reversed1[len1++] = Alignment.GAP;
+ reversed2[len2++] = a2[--j];
+ reversed3[len3++] = Markups.GAP;
+ gaps++;
+ }
+ break;
+ case Directions.STOP:
+ stillGoing = false;
+ }
+ }
+
+ alignment.setSequence1(reverse(reversed1, len1));
+ alignment.setStart1(i);
+ alignment.setSequence2(reverse(reversed2, len2));
+ alignment.setStart2(j);
+ alignment.setMarkupLine(reverse(reversed3, len3));
+ alignment.setIdentity(identity);
+ alignment.setGaps(gaps);
+ alignment.setSimilarity(similarity);
+
+ logger.info("Finished in " + (System.currentTimeMillis() - start)
+ + " milliseconds");
+ return alignment;
+ }
+
+ /**
+ * Returns the maximum of 4 float numbers.
+ *
+ * @param a
+ * float #1
+ * @param b
+ * float #2
+ * @param c
+ * float #3
+ * @param d
+ * float #4
+ * @return The maximum of a, b, c and d.
+ */
+ private static float maximum(float a, float b, float c, float d) {
+ if (a > b) {
+ if (a > c) {
+ return a > d ? a : d;
+ } else {
+ return c > d ? c : d;
+ }
+ } else if (b > c) {
+ return b > d ? b : d;
+ } else {
+ return c > d ? c : d;
+ }
+ }
+
+ /**
+ * Reverses an array of chars
+ *
+ * @param a
+ * @param len
+ * @return the input array of char reserved
+ */
+ private static char[] reverse(char[] a, int len) {
+ char[] b = new char[len];
+ for (int i = len - 1, j = 0; i >= 0; i--, j++) {
+ b[j] = a[i];
+ }
+ return b;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/example/Example.java b/src/jaligner/example/Example.java
new file mode 100644
index 0000000..ab213c7
--- /dev/null
+++ b/src/jaligner/example/Example.java
@@ -0,0 +1,112 @@
+/*
+ * $Id: Example.java,v 1.3 2005/04/03 19:38:21 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.example;
+
+import jaligner.Alignment;
+import jaligner.Sequence;
+import jaligner.SmithWatermanGotoh;
+import jaligner.formats.Pair;
+import jaligner.matrix.MatrixLoader;
+import jaligner.util.SequenceParser;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Example of using JAligner API to align P53 human aganist
+ * P53 mouse using Smith-Waterman-Gotoh algorithm.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class Example {
+
+ /**
+ *
+ */
+ private static final String SAMPLE_SEQUENCE_P35_HUMAN = "jaligner/example/sequences/p53_human.fasta";
+
+ /**
+ *
+ */
+ private static final String SAMPLE_SEQUENCE_P35_MOUSE = "jaligner/example/sequences/p53_mouse.fasta";
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger.getLogger(Example.class.getName());
+
+ /**
+ *
+ * @param args
+ */
+ public static void main(String[] args) {
+ try {
+ logger.info("Running example...");
+
+ Sequence s1 = SequenceParser.parse(loadP53Human());
+ Sequence s2 = SequenceParser.parse(loadP53Mouse());
+
+ Alignment alignment = SmithWatermanGotoh.align(s1, s2, MatrixLoader.load("BLOSUM62"), 10f, 0.5f);
+
+ System.out.println ( alignment.getSummary() );
+ System.out.println ( new Pair().format(alignment) );
+
+ logger.info("Finished running example");
+ } catch (Exception e) {
+ logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e);
+ }
+ }
+
+ /**
+ *
+ * @param path location of the sequence
+ * @return sequence string
+ * @throws IOException
+ */
+ private static String loadSampleSequence(String path) throws IOException {
+ InputStream inputStream = Example.class.getClassLoader().getResourceAsStream(path);
+ StringBuffer buffer = new StringBuffer();
+ int ch;
+ while ((ch = inputStream.read()) != -1) {
+ buffer.append((char)ch);
+ }
+ return buffer.toString();
+ }
+
+ /**
+ *
+ * @return sequence string
+ * @throws IOException
+ */
+ public static String loadP53Human( ) throws IOException {
+ return loadSampleSequence(SAMPLE_SEQUENCE_P35_HUMAN);
+ }
+
+ /**
+ *
+ * @return sequence string
+ * @throws IOException
+ */
+ public static String loadP53Mouse( ) throws IOException {
+ return loadSampleSequence(SAMPLE_SEQUENCE_P35_MOUSE);
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/example/package.html b/src/jaligner/example/package.html
new file mode 100644
index 0000000..c42043b
--- /dev/null
+++ b/src/jaligner/example/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.1 2005/04/05 13:43:32 ahmed Exp $--></head>
+<body bgcolor="white">
+Example for using API of JAligner to perform pairwise sequence alignment.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/example/sequences/p53_human.fasta b/src/jaligner/example/sequences/p53_human.fasta
new file mode 100644
index 0000000..d5f776a
--- /dev/null
+++ b/src/jaligner/example/sequences/p53_human.fasta
@@ -0,0 +1,7 @@
+>p53_human
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
+PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
+CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
+TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACAGR
+DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
+KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
\ No newline at end of file
diff --git a/src/jaligner/example/sequences/p53_mouse.fasta b/src/jaligner/example/sequences/p53_mouse.fasta
new file mode 100644
index 0000000..65e7f3b
--- /dev/null
+++ b/src/jaligner/example/sequences/p53_mouse.fasta
@@ -0,0 +1,8 @@
+>p53_mouse
+MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEA
+LRVSGAPAAQDPVTETPGPAAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVM
+CTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCS
+DGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCM
+GGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGS
+AKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSR
+AHSSYLKTKKGQSTSRHKKTMVKKVGPDSD
\ No newline at end of file
diff --git a/src/jaligner/formats/CLUSTAL.java b/src/jaligner/formats/CLUSTAL.java
new file mode 100644
index 0000000..5630321
--- /dev/null
+++ b/src/jaligner/formats/CLUSTAL.java
@@ -0,0 +1,121 @@
+/*
+ * $Id: CLUSTAL.java,v 1.15 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.formats;
+
+import jaligner.Alignment;
+
+/**
+ * CLUSTAL format.
+ * Example:
+ * <pre>
+ * <small>
+ * CLUSTAL_FORMAT W(1.60) multiple sequence alignment
+ *
+ *
+ * JC2395 NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
+ * KPEL_DROME MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
+ * FASA_MOUSE NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
+ *
+ *
+ * JC2395 -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
+ * KPEL_DROME -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
+ * FASA_MOUSE -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
+ *
+ *
+ * JC2395 IAEEIQAM
+ * KPEL_DROME AMRLIKDY
+ * FASA_MOUSE TLDKFQDM
+ * </small>
+ * </pre>
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class CLUSTAL extends Format {
+
+ /**
+ * Name width
+ */
+ private static final int NAME_WIDTH = 36;
+
+ /**
+ * Sequence width
+ */
+ private static final int SEQUENCE_WIDTH = 50;
+
+ /**
+ * CLUSTAL header
+ */
+ private static final String HEADER = "CLUSTAL_FORMAT W(1.60) multiple sequence alignment\n\n";
+
+ /**
+ * Constructor
+ */
+ public CLUSTAL() {
+ super( );
+ setId("CLUSTAL");
+ }
+
+ /**
+ * Returns CLUSTAL format
+ * @param names array of the names of the sequences.
+ * @param sequences array of the sequences
+ */
+ public String format(String[] names, String[] sequences) {
+ StringBuffer buffer = new StringBuffer (HEADER);
+ int maxSequenceLength = 0;
+ for (int i = 0; i < sequences.length; i++) {
+ if (sequences[i].length() > maxSequenceLength) {
+ maxSequenceLength = sequences[i].length();
+ }
+ }
+
+ for (int i = 0; i * SEQUENCE_WIDTH < maxSequenceLength; i++) {
+
+ for (int j = 0; j < sequences.length; j++) {
+ buffer.append( NAME_WIDTH <= names[j].length() ? names[j].substring(0, NAME_WIDTH - 1) : names[j] );
+ for (int k = names[j].length(); k < NAME_WIDTH; k++) {
+ buffer.append(" ");
+ }
+ if (names[j].length() >= NAME_WIDTH) {
+ buffer.append(" ");
+ }
+ buffer.append(sequences[j].substring(i * SEQUENCE_WIDTH, ((i + 1) * SEQUENCE_WIDTH) < sequences[j].length() ? (i + 1) * SEQUENCE_WIDTH: sequences[j].length()));
+ if (j < sequences.length) {
+ buffer.append("\n");
+ }
+ }
+ if ((i + 1) * SEQUENCE_WIDTH < maxSequenceLength) {
+ buffer.append("\n\n");
+ }
+ }
+ return buffer.toString();
+ }
+
+ /**
+ * Returns CLUSTAL format of the alignment
+ * @param alignment ({@link Alignment})
+ * @return CLUSTAL format of the alignment
+ */
+ public String format (Alignment alignment) {
+ String[] sequences = {new String(alignment.getSequence1()), new String(alignment.getSequence2())};
+ String[] names = {alignment.getName1(), alignment.getName2()};
+ return format (names, sequences);
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/formats/FASTA.java b/src/jaligner/formats/FASTA.java
new file mode 100644
index 0000000..2a3b3f3
--- /dev/null
+++ b/src/jaligner/formats/FASTA.java
@@ -0,0 +1,79 @@
+/*
+ * $Id: FASTA.java,v 1.19 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.formats;
+
+import jaligner.Alignment;
+import jaligner.Sequence;
+
+/**
+ * <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class FASTA extends Format {
+
+ /**
+ * Number of characters per line
+ */
+ private static final int LINE_WIDTH = 60;
+
+ /**
+ * Constructor for FASTA.
+ */
+ public FASTA() {
+ super( );
+ setId("FASTA");
+ }
+
+ /**
+ * Returns the name, description and sequence combined in one string.
+ * The length of each line in the sequence is FASTA.LINE_LENGTH
+ *
+ * @return String
+ */
+ public String format (Sequence sequence) {
+ StringBuffer buffer = new StringBuffer (">");
+ buffer.append(sequence.getId() == null ? "" : sequence.getId());
+ buffer.append("\n");
+ for (int i = 0, n = sequence.length(); i * LINE_WIDTH < n; i++) {
+ for (int j = i * LINE_WIDTH, m = (i + 1) * LINE_WIDTH < n ? (i + 1) * LINE_WIDTH: n; j < m; j++) {
+ buffer.append(sequence.subsequence(j, 1));
+ }
+ buffer.append("\n");
+ }
+ return buffer.toString( );
+ }
+
+ /**
+ *
+ * @param alignment
+ * @return FASTA format of the input alignment
+ */
+ public String format (Alignment alignment) {
+ StringBuffer buffer = new StringBuffer();
+ StringBuffer s1 = new StringBuffer();
+ StringBuffer s2 = new StringBuffer();
+ s1.append(alignment.getSequence1());
+ s2.append(alignment.getSequence2());
+ buffer.append(format(new Sequence(s1.toString(), alignment.getName1(), "", Sequence.PROTEIN)));
+ buffer.append(format(new Sequence(s2.toString(), alignment.getName2(), "", Sequence.PROTEIN)));
+ return buffer.toString();
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/formats/Format.java b/src/jaligner/formats/Format.java
new file mode 100644
index 0000000..f59cdae
--- /dev/null
+++ b/src/jaligner/formats/Format.java
@@ -0,0 +1,59 @@
+/*
+ * $Id: Format.java,v 1.4 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.formats;
+
+import jaligner.Alignment;
+
+/**
+ * Abstract format
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public abstract class Format {
+
+ /**
+ * Format id
+ */
+ private String id = null;
+
+ /**
+ * Formats alignment
+ * @param alignment
+ * @return formatted alignment
+ * @see Alignment
+ */
+ public abstract String format(Alignment alignment);
+
+ /**
+ * Sets format id
+ * @param id to set
+ */
+ public void setId (String id) {
+ this.id = id;
+ }
+
+ /**
+ * Returns format id
+ * @return id
+ */
+ public String getId ( ) {
+ return this.id == null ? this.getClass().getName() : this.id;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/formats/FormatFactory.java b/src/jaligner/formats/FormatFactory.java
new file mode 100644
index 0000000..ba884de
--- /dev/null
+++ b/src/jaligner/formats/FormatFactory.java
@@ -0,0 +1,84 @@
+/*
+ * $Id: FormatFactory.java,v 1.7 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.formats;
+
+import java.util.Collection;
+import java.util.HashMap;
+
+/**
+ * Formats factory.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class FormatFactory {
+ /**
+ * Instance of {@link FormatFactory}
+ */
+ private static FormatFactory instance = null;
+
+ /**
+ * {@link HashMap} of {@link Format}
+ */
+ private HashMap formats = new HashMap();
+
+ /**
+ * Hidden constructor
+ *
+ */
+ private FormatFactory ( ) {
+ super();
+ }
+
+ /**
+ * Returns an instance for {@link FormatFactory}.
+ * @return {@link FormatFactory}
+ */
+ public static FormatFactory getInstance() {
+ if (instance == null) {
+ instance = new FormatFactory();
+ }
+ return instance;
+ }
+
+ /**
+ * Registers format.
+ * @param format instance of format
+ */
+ public void registerFormat(Format format) {
+ formats.put(format.getId(), format);
+ }
+
+ /**
+ * Returns an instance of {@link Format}.
+ * @param id format id
+ * @return {@link Format} or null if id not found
+ */
+ public Format getFormat(String id) {
+ return (Format) formats.get(id);
+ }
+
+ /**
+ * Returns a list of registered formats
+ * @return {@link Collection}
+ */
+ public Collection getFormats( ) {
+ return formats.keySet();
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/formats/Pair.java b/src/jaligner/formats/Pair.java
new file mode 100644
index 0000000..cf707bb
--- /dev/null
+++ b/src/jaligner/formats/Pair.java
@@ -0,0 +1,191 @@
+/*
+ * $Id: Pair.java,v 1.18 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.formats;
+
+import jaligner.Alignment;
+import jaligner.util.Commons;
+
+/**
+ * <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class Pair extends Format {
+
+ /**
+ * Name width
+ */
+ private static final int NAME_WIDTH = 13;
+
+ /**
+ * Position width
+ */
+ private static final int POSITION_WIDTH = 6;
+
+ /**
+ * Sequence width
+ */
+ private static final int SEQUENCE_WIDTH = 50;
+
+ /**
+ * Space
+ */
+ private static final String BLANK = " ";
+
+ /**
+ * Constructor
+ *
+ */
+ public Pair( ) {
+ super();
+ setId("Pair");
+ }
+
+ /**
+ * Formats an alignment object to the Pair_FORMAT format
+ * @param alignment alignment object to be formated
+ * @return string of the alignment pair-formatted
+ */
+ public String format(Alignment alignment) {
+ char[] sequence1 = alignment.getSequence1();
+ char[] sequence2 = alignment.getSequence2();
+ char[] markup = alignment.getMarkupLine();
+
+ int length = sequence1.length > sequence2.length ? sequence2.length : sequence1.length;
+
+ String name1 = adjustName(alignment.getName1());
+ String name2 = adjustName(alignment.getName2());
+
+ StringBuffer buffer = new StringBuffer ( );
+
+ StringBuffer preMarkup = new StringBuffer ( );
+ for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++) {
+ preMarkup.append(BLANK);
+ }
+
+ int oldPosition1, position1 = 1 + alignment.getStart1();
+ int oldPosition2, position2 = 1 + alignment.getStart2();
+
+ char[] subsequence1;
+ char[] subsequence2;
+ char[] submarkup;
+ int line;
+
+ char c1, c2;
+
+ for (int i = 0; i * SEQUENCE_WIDTH < length; i++) {
+
+ oldPosition1 = position1;
+ oldPosition2 = position2;
+
+ line = ((i + 1) * SEQUENCE_WIDTH) < length ? (i + 1) * SEQUENCE_WIDTH: length;
+
+ subsequence1 = new char[line - i * SEQUENCE_WIDTH];
+ subsequence2 = new char[line - i * SEQUENCE_WIDTH];
+ submarkup = new char[line - i * SEQUENCE_WIDTH];
+
+ for (int j = i * SEQUENCE_WIDTH, k = 0; j < line; j++, k++) {
+ subsequence1[k] = sequence1[j];
+ subsequence2[k] = sequence2[j];
+ submarkup[k] = markup[j];
+ c1 = subsequence1[k];
+ c2 = subsequence2[k];
+ if (c1 == c2) {
+ position1++;
+ position2++;
+ } else if (c1 == Alignment.GAP) {
+ position2++;
+ } else if (c2 == Alignment.GAP) {
+ position1++;
+ } else {
+ position1++;
+ position2++;
+ }
+ }
+
+ buffer.append(name1);
+ buffer.append(BLANK);
+ buffer.append(adjustPosition(new Integer(oldPosition1).toString()));
+ buffer.append(BLANK);
+ buffer.append(subsequence1);
+ buffer.append(BLANK);
+ buffer.append(adjustPosition(new Integer(position1 - 1).toString()));
+ buffer.append(Commons.getLineSeparator());
+
+ buffer.append(preMarkup);
+ buffer.append(submarkup);
+ buffer.append(Commons.getLineSeparator());
+
+ buffer.append(name2);
+ buffer.append(BLANK);
+ buffer.append(adjustPosition(new Integer(oldPosition2).toString()));
+ buffer.append(BLANK);
+ buffer.append(subsequence2);
+ buffer.append(BLANK);
+ buffer.append(adjustPosition(new Integer(position2 - 1).toString()));
+ buffer.append(Commons.getLineSeparator());
+
+ buffer.append(Commons.getLineSeparator());
+ }
+ return buffer.toString();
+ }
+
+ /**
+ *
+ * @param name name to adjusted
+ * @return adjusted name
+ */
+ private String adjustName(String name) {
+ StringBuffer buffer = new StringBuffer ( );
+
+ if (name.length() > NAME_WIDTH) {
+ buffer.append(name.substring(0, NAME_WIDTH));
+ } else {
+ buffer.append(name);
+ for (int j = buffer.length(); j < NAME_WIDTH; j++) {
+ buffer.append (BLANK);
+ }
+ }
+ return buffer.toString();
+ }
+
+ /**
+ *
+ * @param position
+ * @return string
+ */
+ private String adjustPosition(String position) {
+ StringBuffer buffer1 = new StringBuffer( );
+ StringBuffer buffer2 = new StringBuffer( );
+
+ if (position.length() > POSITION_WIDTH) {
+ buffer1.append(position.substring(position.length() - POSITION_WIDTH, position.length()));
+ } else {
+ buffer1.append(position);
+ }
+
+ for (int j = 0, n = POSITION_WIDTH - buffer1.length(); j < n; j++) {
+ buffer2.append(BLANK);
+ }
+
+ buffer2.append(buffer1.toString());
+ return buffer2.toString();
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/formats/package.html b/src/jaligner/formats/package.html
new file mode 100644
index 0000000..5b3633b
--- /dev/null
+++ b/src/jaligner/formats/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.5 2004/11/30 02:00:56 ahmed Exp $--></head>
+<body bgcolor="white">
+Group of formats for output alignments.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/matrix/MatricesCompartor.java b/src/jaligner/matrix/MatricesCompartor.java
new file mode 100644
index 0000000..6aedcdd
--- /dev/null
+++ b/src/jaligner/matrix/MatricesCompartor.java
@@ -0,0 +1,68 @@
+/*
+ * $Id: MatricesCompartor.java,v 1.1 2005/01/11 16:48:25 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.matrix;
+
+import java.util.Comparator;
+
+/**
+ * Comparator to sort the scoring matrices by their names.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class MatricesCompartor implements Comparator {
+
+ /* (non-Javadoc)
+ * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
+ */
+ public int compare(Object o1, Object o2) {
+ String s1 = (String) o1;
+ String s2 = (String) o2;
+
+ int index1 = firstDigitIndex(s1);
+ int index2 = firstDigitIndex(s2);
+
+ if (index1 == -1 || index2 == -1) {
+ return s1.compareToIgnoreCase(s2);
+ } else {
+ String s3 = s1.substring(0, index1);
+ String s4 = s2.substring(0, index2);
+ if (s3.equalsIgnoreCase(s4)) {
+ return new Integer(s1.substring(index1)).compareTo(new Integer(s2.substring(index2)));
+ } else {
+ return s1.compareToIgnoreCase(s2);
+ }
+ }
+ }
+
+ /**
+ * Returns the index of the first digit in a String.
+ * If there are no digits, returns -1.
+ * @param s String to be searched for the digits in
+ * @return int
+ */
+ private int firstDigitIndex (String s) {
+ for (int i = 0; i < s.length(); i++) {
+ if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
+ return i;
+ }
+ }
+ return -1;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/matrix/Matrix.java b/src/jaligner/matrix/Matrix.java
new file mode 100644
index 0000000..79ae0e3
--- /dev/null
+++ b/src/jaligner/matrix/Matrix.java
@@ -0,0 +1,73 @@
+/*
+ * $Id: Matrix.java,v 1.2 2005/04/14 14:44:42 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.matrix;
+
+import java.io.Serializable;
+
+/**
+ * Scoring matrix.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class Matrix implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3833742170619524400L;
+
+ /**
+ * Matrix id (or name)
+ */
+ private String id = null;
+
+ /**
+ * Scores
+ */
+ private float[][] scores = null;
+
+ public Matrix(String id, float[][] scores) {
+ this.id = id;
+ this.scores = scores;
+ }
+
+ /**
+ * @return Returns the id.
+ */
+ public String getId() {
+ return this.id;
+ }
+
+ /**
+ * @return Returns the scores.
+ */
+ public float[][] getScores() {
+ return this.scores;
+ }
+
+ /**
+ *
+ * @param a
+ * @param b
+ * @return score
+ */
+ public float getScore(char a, char b) {
+ return this.scores[a][b];
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/matrix/MatrixLoader.java b/src/jaligner/matrix/MatrixLoader.java
new file mode 100644
index 0000000..94c4eff
--- /dev/null
+++ b/src/jaligner/matrix/MatrixLoader.java
@@ -0,0 +1,220 @@
+/*
+ * $Id: MatrixLoader.java,v 1.2 2005/01/25 11:54:30 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.matrix;
+
+import jaligner.ui.filechooser.NamedInputStream;
+import jaligner.util.Commons;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.JarURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.jar.JarEntry;
+import java.util.jar.JarFile;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Scoring matrices loader from a jar file or a file system.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class MatrixLoader {
+ /**
+ * The starter character of a comment line.
+ */
+ private static final char COMMENT_STARTER = '#';
+
+ /**
+ * The size of the scoring matrix. It is the number of the characters in the ASCII table.
+ * It is more than the 20 amino acids just to save the processing time of the mapping.
+ */
+ private static final int SIZE = 127;
+
+ /**
+ * The path to the matrices within the package.
+ */
+ private static final String MATRICES_HOME = "jaligner/matrix/matrices/";
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger.getLogger(MatrixLoader.class.getName());
+
+ /**
+ * Loads scoring matrix from Jar file or file system.
+ * @param matrix to load
+ * @return loaded matrix
+ * @throws MatrixLoaderException
+ * @see Matrix
+ */
+ public static Matrix load (String matrix) throws MatrixLoaderException {
+ InputStream is = null;
+
+ if (new StringTokenizer(matrix, Commons.getFileSeparator()).countTokens() == 1) {
+ // Matrix does not include the path
+ // Load the matrix from matrices.jar
+ is = MatrixLoader.class.getClassLoader().getResourceAsStream(MATRICES_HOME + matrix);
+ } else {
+ // Matrix includes the path information
+ // Load the matrix from the file system
+ try {
+ is = new FileInputStream(matrix);
+ } catch (Exception e) {
+ String message = "Failed opening input stream: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ throw new MatrixLoaderException (message);
+ }
+ }
+
+ return load(new NamedInputStream(matrix, is));
+ }
+
+ /**
+ * Loads scoring matrix from {@link InputStream}
+ * @param nis named input stream
+ * @return loaded matrix
+ * @throws MatrixLoaderException
+ * @see Matrix
+ * @see NamedInputStream
+ */
+ public static Matrix load (NamedInputStream nis) throws MatrixLoaderException {
+ logger.info("Loading scoring matrix...");
+ char[] acids = new char[SIZE];
+
+ // Initialize the acids array to null values (ascii = 0)
+ for (int i = 0; i < SIZE; i++) {
+ acids[i] = 0;
+ }
+
+ float[][] scores = new float[SIZE][SIZE];
+
+ BufferedReader reader = new BufferedReader(new InputStreamReader(nis.getInputStream()));
+
+ String line;
+
+ try {
+ // Skip the comment lines
+ while ((line = reader.readLine()) != null && line.trim().charAt(0) == COMMENT_STARTER);
+ } catch (Exception e) {
+ String message = "Failed reading from input stream: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ throw new MatrixLoaderException (message);
+ }
+
+ // Read the headers line (the letters of the acids)
+ StringTokenizer tokenizer;
+ tokenizer = new StringTokenizer ( line.trim( ) );
+ for (int j = 0; tokenizer.hasMoreTokens(); j++) {
+ acids[j] = tokenizer.nextToken().charAt(0);
+ }
+
+ try {
+ // Read the scores
+ while ((line = reader.readLine()) != null) {
+ tokenizer = new StringTokenizer ( line.trim( ) );
+ char acid = tokenizer.nextToken().charAt(0);
+ for (int i = 0; i < SIZE; i++) {
+ if (acids[i] != 0) {
+ scores[acid][acids[i]] = Float.parseFloat(tokenizer.nextToken());
+ }
+ }
+ }
+ } catch (Exception e) {
+ String message = "Failed reading from input stream: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ throw new MatrixLoaderException (message);
+ }
+ logger.info("Finished loading scoring matrix");
+ return new Matrix(nis.getName(), scores);
+ }
+
+ /**
+ * Returns a list of the scoring matrices in the matrices home directory
+ * @param sort flag to sort the list or not
+ * @return sorted array of scoring matrices
+ * @throws MatrixLoaderException
+ */
+ public static Collection list (boolean sort ) throws MatrixLoaderException {
+ logger.info("Loading list of scoring matrices...");
+ ArrayList matrices = new ArrayList();
+ URL url = MatrixLoader.class.getClassLoader().getResource(MATRICES_HOME);
+ if (url.getFile().toString().indexOf("!") != -1) {
+ // Load from Jar
+ JarURLConnection connection = null;
+ JarFile jar = null;
+ try {
+ connection = (JarURLConnection) url.openConnection();
+ jar = connection.getJarFile();
+ } catch (Exception e) {
+ String message = "Failed opening a connection to jar: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ throw new MatrixLoaderException (message);
+ }
+ Enumeration entries = jar.entries();
+ JarEntry entry;
+ String entryName;
+ int length = MATRICES_HOME.length();
+ while (entries.hasMoreElements()) {
+ entry = (JarEntry) entries.nextElement();
+ if (!entry.isDirectory()) {
+ entryName = entry.getName();
+ if (entryName.startsWith(MATRICES_HOME)) {
+ matrices.add(entryName.substring(length));
+ }
+ }
+ }
+ } else {
+ // Load from file system
+ String home = url.getFile( );
+ File dir = new File (home);
+ String files[] = dir.list( );
+ File file;
+ for (int i = 0, n = files.length; i < n; i++) {
+ file = new File (home + files[i]);
+ if (file.isFile() && file.canRead()) {
+ matrices.add(file.getName());
+ }
+ }
+ }
+ if (sort) {
+ Collections.sort(matrices, new MatricesCompartor());
+ }
+ logger.info("Finished loading list of scoring matrices");
+ return matrices;
+ }
+
+ /**
+ * Returns a list of the scoring matrices in the matrices home directory
+ * @return sorted array of scoring matrices
+ * @throws MatrixLoaderException
+ */
+ public static Collection list ( ) throws MatrixLoaderException {
+ return list(false);
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/matrix/MatrixLoaderException.java b/src/jaligner/matrix/MatrixLoaderException.java
new file mode 100644
index 0000000..a62783b
--- /dev/null
+++ b/src/jaligner/matrix/MatrixLoaderException.java
@@ -0,0 +1,39 @@
+/*
+ * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.matrix;
+
+/**
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class MatrixLoaderException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3906364935142586680L;
+
+ /**
+ * @param message
+ */
+ public MatrixLoaderException(String message) {
+ super(message);
+ }
+}
diff --git a/src/jaligner/matrix/matrices/BLOSUM100 b/src/jaligner/matrix/matrices/BLOSUM100
new file mode 100644
index 0000000..4063c3b
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM100
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum100_3.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 100
+# Entropy = 1.4516, Expected = -1.0948
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10
+R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10
+N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10
+D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10
+C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10
+Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10
+E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10
+G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10
+H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10
+I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10
+L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10
+K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10
+M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10
+F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10
+P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10
+S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10
+T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10
+W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10
+Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10
+V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10
+B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10
+Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10
+X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM30 b/src/jaligner/matrix/matrices/BLOSUM30
new file mode 100644
index 0000000..abf2edb
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM30
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum30.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/5 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 30
+# Entropy = 0.1424, Expected = -0.1074
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7
+R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7
+N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7
+D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7
+C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7
+Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7
+E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7
+G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7
+H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7
+I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7
+L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7
+K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7
+M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7
+F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7
+P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7
+S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7
+T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7
+W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7
+Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7
+V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7
+B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7
+Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7
+X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM35 b/src/jaligner/matrix/matrices/BLOSUM35
new file mode 100644
index 0000000..a00a9b5
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM35
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum35.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 35
+# Entropy = 0.2111, Expected = -0.1550
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5
+R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5
+N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5
+D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5
+C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5
+Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5
+E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5
+G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5
+H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5
+I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5
+L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5
+K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5
+M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5
+F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5
+P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5
+S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5
+T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5
+W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5
+Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5
+V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5
+B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5
+Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5
+X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM40 b/src/jaligner/matrix/matrices/BLOSUM40
new file mode 100644
index 0000000..41e1c63
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM40
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum40.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 40
+# Entropy = 0.2851, Expected = -0.2090
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6
+R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6
+N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6
+D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6
+C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6
+Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6
+E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6
+G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6
+H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6
+I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6
+L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6
+K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6
+M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6
+F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6
+P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6
+S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6
+T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6
+W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6
+Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6
+V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6
+B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6
+Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM45 b/src/jaligner/matrix/matrices/BLOSUM45
new file mode 100644
index 0000000..ece78b5
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM45
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum45.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 45
+# Entropy = 0.3795, Expected = -0.2789
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5
+R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
+N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
+D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5
+Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
+E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5
+G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5
+H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5
+I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5
+L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5
+K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5
+M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5
+F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5
+P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5
+Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5
+V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5
+B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
+Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM50 b/src/jaligner/matrix/matrices/BLOSUM50
new file mode 100644
index 0000000..62592f3
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM50
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum50.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 50
+# Entropy = 0.4808, Expected = -0.3573
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5
+N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5
+D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5
+C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5
+Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5
+E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5
+G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5
+H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5
+I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5
+L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5
+K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5
+M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5
+F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5
+P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5
+S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5
+W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5
+Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5
+V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5
+B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5
+Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5
+X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM55 b/src/jaligner/matrix/matrices/BLOSUM55
new file mode 100644
index 0000000..4a06659
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM55
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum55.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 55
+# Entropy = 0.5637, Expected = -0.4179
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5
+R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5
+D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5
+C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5
+Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
+E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5
+G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5
+H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5
+I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5
+L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5
+K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5
+M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
+F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5
+P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5
+S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5
+W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5
+Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5
+V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5
+B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5
+Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5
+X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM60 b/src/jaligner/matrix/matrices/BLOSUM60
new file mode 100644
index 0000000..45e86ca
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM60
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum60.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 60
+# Entropy = 0.6603, Expected = -0.4917
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
+R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4
+N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
+D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
+C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
+E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4
+L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4
+K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4
+V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
+B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4
+Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM62 b/src/jaligner/matrix/matrices/BLOSUM62
new file mode 100644
index 0000000..acb602d
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM62
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum62.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 62
+# Entropy = 0.6979, Expected = -0.5209
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
+R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
+N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
+D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
+C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
+V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
+B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
+Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM65 b/src/jaligner/matrix/matrices/BLOSUM65
new file mode 100644
index 0000000..9211c16
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM65
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum65.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 65
+# Entropy = 0.7576, Expected = -0.5675
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5
+D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5
+C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5
+Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5
+G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5
+H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5
+L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5
+M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
+F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5
+P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5
+Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5
+V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5
+B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5
+Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5
+X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM70 b/src/jaligner/matrix/matrices/BLOSUM70
new file mode 100644
index 0000000..4a05223
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM70
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum70.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 70
+# Entropy = 0.8391, Expected = -0.6313
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5
+D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5
+C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5
+Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5
+E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
+G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
+H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5
+I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5
+L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5
+M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
+F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
+P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5
+S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5
+Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5
+V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5
+B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5
+Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5
+X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM75 b/src/jaligner/matrix/matrices/BLOSUM75
new file mode 100644
index 0000000..1dcf308
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM75
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum75.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 75
+# Entropy = 0.9077, Expected = -0.6845
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
+R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
+N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5
+D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5
+C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5
+Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5
+E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
+G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
+H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5
+I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5
+L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5
+M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5
+F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
+P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5
+S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5
+Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5
+V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5
+B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5
+Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5
+X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM80 b/src/jaligner/matrix/matrices/BLOSUM80
new file mode 100644
index 0000000..d7c998b
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM80
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum80_3.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 80
+# Entropy = 0.9868, Expected = -0.7442
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8
+R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8
+N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8
+D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8
+C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8
+Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8
+E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8
+G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8
+H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8
+I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8
+L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8
+K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8
+M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8
+F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8
+P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8
+S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8
+T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8
+W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8
+Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8
+V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8
+B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8
+Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8
+X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM85 b/src/jaligner/matrix/matrices/BLOSUM85
new file mode 100644
index 0000000..132ff2c
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM85
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum85.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 85
+# Entropy = 1.0805, Expected = -0.8153
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6
+R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6
+N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
+D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6
+C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6
+Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6
+E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6
+G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6
+H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6
+I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6
+L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
+K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6
+M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6
+F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6
+P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6
+S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6
+T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6
+W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6
+Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6
+V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6
+B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6
+Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
+X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/src/jaligner/matrix/matrices/BLOSUM90 b/src/jaligner/matrix/matrices/BLOSUM90
new file mode 100644
index 0000000..d5fc9e0
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUM90
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosum90.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 90
+# Entropy = 1.1806, Expected = -0.8887
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -1 -1 -6
+R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 0 -2 -6
+N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
+D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6
+C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6
+Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6
+E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6
+G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6
+H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6
+I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6
+L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
+K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6
+M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6
+F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6
+P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6
+S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -1 -1 -6
+T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -1 -1 -6
+W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -4 -3 -6
+Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6
+V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6
+B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6
+Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
+X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/src/jaligner/matrix/matrices/BLOSUMN b/src/jaligner/matrix/matrices/BLOSUMN
new file mode 100644
index 0000000..0dba279
--- /dev/null
+++ b/src/jaligner/matrix/matrices/BLOSUMN
@@ -0,0 +1,31 @@
+# Matrix made by matblas from blosumn.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= -2
+# Entropy = 1.5172, Expected = -1.1484
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -2 -2 -3 -2 -1 -2 -1 -3 -3 -3 -2 -2 -4 -1 1 -1 -4 -4 -1 -3 -2 -1 -7
+R -2 7 -1 -3 -6 0 -2 -4 -1 -5 -4 2 -3 -4 -3 -2 -2 -5 -4 -4 -2 -1 -2 -7
+N -2 -1 7 1 -4 -1 -1 -2 0 -5 -5 -1 -4 -5 -4 0 -1 -6 -4 -4 4 -1 -2 -7
+D -3 -3 1 7 -6 -2 1 -3 -2 -6 -6 -2 -5 -5 -3 -2 -2 -7 -5 -5 4 0 -3 -7
+C -2 -6 -4 -6 9 -5 -7 -5 -6 -2 -3 -5 -3 -3 -5 -2 -2 -5 -4 -2 -5 -6 -4 -7
+Q -1 0 -1 -2 -5 7 1 -4 0 -4 -3 1 -1 -4 -2 -1 -2 -4 -3 -4 -1 4 -2 -7
+E -2 -2 -1 1 -7 1 6 -4 -1 -5 -5 0 -4 -5 -3 -1 -2 -5 -4 -4 0 5 -2 -7
+G -1 -4 -2 -3 -5 -4 -4 6 -4 -6 -6 -3 -5 -5 -4 -1 -3 -5 -6 -5 -2 -4 -3 -7
+H -3 -1 0 -2 -6 0 -1 -4 9 -5 -4 -2 -3 -3 -4 -2 -3 -4 1 -5 -1 -1 -3 -7
+I -3 -5 -5 -6 -2 -4 -5 -6 -5 6 1 -4 1 -1 -5 -4 -2 -4 -3 2 -5 -5 -2 -7
+L -3 -4 -5 -6 -3 -3 -5 -6 -4 1 5 -4 2 0 -5 -4 -3 -4 -3 0 -5 -4 -2 -7
+K -2 2 -1 -2 -5 1 0 -3 -2 -4 -4 6 -2 -4 -2 -1 -2 -6 -4 -4 -1 0 -2 -7
+M -2 -3 -4 -5 -3 -1 -4 -5 -3 1 2 -2 8 -1 -4 -3 -2 -2 -3 0 -5 -3 -2 -7
+F -4 -4 -5 -5 -3 -4 -5 -5 -3 -1 0 -4 -1 7 -5 -4 -3 0 3 -2 -5 -5 -3 -7
+P -1 -3 -4 -3 -5 -2 -3 -4 -4 -5 -5 -2 -4 -5 8 -2 -3 -5 -5 -4 -4 -3 -3 -7
+S 1 -2 0 -2 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 6 1 -4 -3 -3 -1 -1 -1 -7
+T -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -3 -2 -2 -3 -3 1 6 -5 -3 -1 -2 -2 -1 -7
+W -4 -5 -6 -7 -5 -4 -5 -5 -4 -4 -4 -6 -2 0 -5 -4 -5 11 1 -3 -6 -4 -4 -7
+Y -4 -4 -4 -5 -4 -3 -4 -6 1 -3 -3 -4 -3 3 -5 -3 -3 1 8 -3 -4 -4 -3 -7
+V -1 -4 -4 -5 -2 -4 -4 -5 -5 2 0 -4 0 -2 -4 -3 -1 -3 -3 5 -5 -4 -2 -7
+B -3 -2 4 4 -5 -1 0 -2 -1 -5 -5 -1 -5 -5 -4 -1 -2 -6 -4 -5 4 1 -2 -7
+Z -2 -1 -1 0 -6 4 5 -4 -1 -5 -4 0 -3 -5 -3 -1 -2 -4 -4 -4 1 4 -2 -7
+X -1 -2 -2 -3 -4 -2 -2 -3 -3 -2 -2 -2 -2 -3 -3 -1 -1 -4 -3 -2 -2 -2 -2 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/jaligner/matrix/matrices/DAYHOFF b/src/jaligner/matrix/matrices/DAYHOFF
new file mode 100644
index 0000000..cf117a1
--- /dev/null
+++ b/src/jaligner/matrix/matrices/DAYHOFF
@@ -0,0 +1,32 @@
+#Date: Wed, 18 Sep 91 17:36:51 EDT
+#From: altschul at ray.nlm.nih.gov (Stephen Altschul)
+#To: gish at ray.nlm.nih.gov
+#Subject: Vanilla-flavored PAM-250
+#
+# substitution scores for B, Z, X, and * were obtained with "pam" version 1.0.5
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -3 0 0 0 0 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
+G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
+F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
+B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/EDNAFULL b/src/jaligner/matrix/matrices/EDNAFULL
new file mode 100644
index 0000000..d35c3a8
--- /dev/null
+++ b/src/jaligner/matrix/matrices/EDNAFULL
@@ -0,0 +1,25 @@
+#
+# This matrix was created by Todd Lowe 12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+# nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+ A T G C S W R Y K M B V H D N U
+A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 -4
+T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
+G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 -4
+C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 -4
+S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4
+W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 1
+R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4
+Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 1
+K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 1
+M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4
+B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1
+V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4
+H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1
+D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1
+N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2
+U -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
diff --git a/src/jaligner/matrix/matrices/GONNET b/src/jaligner/matrix/matrices/GONNET
new file mode 100644
index 0000000..038de69
--- /dev/null
+++ b/src/jaligner/matrix/matrices/GONNET
@@ -0,0 +1,26 @@
+# PAM 250 matrix recommended by Gonnet, Cohen & Benner
+# Science June 5, 1992.
+# Values rounded to nearest integer
+ C S T P A G N D E Q H R K M I L V F Y W X *
+C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8
+S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8
+T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8
+P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8
+A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8
+G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8
+N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8
+D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8
+E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8
+Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8
+H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8
+R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8
+K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8
+M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8
+I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8
+L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8
+V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8
+F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8
+Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8
+W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8
+X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/IDENTITY b/src/jaligner/matrix/matrices/IDENTITY
new file mode 100644
index 0000000..1f22fab
--- /dev/null
+++ b/src/jaligner/matrix/matrices/IDENTITY
@@ -0,0 +1,25 @@
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
+A 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+R -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+N -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+B -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+D -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+C -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+Q -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+Z -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+E -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+G -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+H -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+I -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+L -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+K -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+M -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+F -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+P -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000
+S -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000
+T -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000
+W -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000
+Y -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000
+V -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000
+X -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 -10000
+* -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0
diff --git a/src/jaligner/matrix/matrices/MATCH b/src/jaligner/matrix/matrices/MATCH
new file mode 100644
index 0000000..1895ac1
--- /dev/null
+++ b/src/jaligner/matrix/matrices/MATCH
@@ -0,0 +1,25 @@
+ A R N B D C Q Z E G H I L K M F P S T W Y V X *
+A 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+R -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+N -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+B -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+D -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+C -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+Q -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+Z -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+E -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+G -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1
+P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1
+S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1
+T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1
+W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1
+Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1
+V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
+* -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
diff --git a/src/jaligner/matrix/matrices/PAM10 b/src/jaligner/matrix/matrices/PAM10
new file mode 100644
index 0000000..202056a
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM10
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 10 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -8.27, Entropy = 3.43 bits
+#
+# Lowest score = -23, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 7 -10 -7 -6 -10 -7 -5 -4 -11 -8 -9 -10 -8 -12 -4 -3 -3 -20 -11 -5 -6 -6 -6 -23
+R -10 9 -9 -17 -11 -4 -15 -13 -4 -8 -12 -2 -7 -12 -7 -6 -10 -5 -14 -11 -11 -7 -9 -23
+N -7 -9 9 -1 -17 -7 -5 -6 -2 -8 -10 -4 -15 -12 -9 -2 -5 -11 -7 -12 7 -6 -6 -23
+D -6 -17 -1 8 -21 -6 0 -6 -7 -11 -19 -8 -17 -21 -12 -7 -8 -21 -17 -11 7 -1 -9 -23
+C -10 -11 -17 -21 10 -20 -20 -13 -10 -9 -21 -20 -20 -19 -11 -6 -11 -22 -7 -9 -18 -20 -13 -23
+Q -7 -4 -7 -6 -20 9 -1 -10 -2 -11 -8 -6 -7 -19 -6 -8 -9 -19 -18 -10 -6 7 -8 -23
+E -5 -15 -5 0 -20 -1 8 -7 -9 -8 -13 -7 -10 -20 -9 -7 -9 -23 -11 -10 -1 7 -8 -23
+G -4 -13 -6 -6 -13 -10 -7 7 -13 -17 -14 -10 -12 -12 -10 -4 -10 -21 -20 -9 -6 -8 -8 -23
+H -11 -4 -2 -7 -10 -2 -9 -13 10 -13 -9 -10 -17 -9 -7 -9 -11 -10 -6 -9 -4 -4 -8 -23
+I -8 -8 -8 -11 -9 -11 -8 -17 -13 9 -4 -9 -3 -5 -12 -10 -5 -20 -9 -1 -9 -9 -8 -23
+L -9 -12 -10 -19 -21 -8 -13 -14 -9 -4 7 -11 -2 -5 -10 -12 -10 -9 -10 -5 -12 -10 -9 -23
+K -10 -2 -4 -8 -20 -6 -7 -10 -10 -9 -11 7 -4 -20 -10 -7 -6 -18 -12 -13 -5 -6 -8 -23
+M -8 -7 -15 -17 -20 -7 -10 -12 -17 -3 -2 -4 12 -7 -11 -8 -7 -19 -17 -4 -16 -8 -9 -23
+F -12 -12 -12 -21 -19 -19 -20 -12 -9 -5 -5 -20 -7 9 -13 -9 -12 -7 -1 -12 -14 -20 -12 -23
+P -4 -7 -9 -12 -11 -6 -9 -10 -7 -12 -10 -10 -11 -13 8 -4 -7 -20 -20 -9 -10 -7 -8 -23
+S -3 -6 -2 -7 -6 -8 -7 -4 -9 -10 -12 -7 -8 -9 -4 7 -2 -8 -10 -10 -4 -8 -6 -23
+T -3 -10 -5 -8 -11 -9 -9 -10 -11 -5 -10 -6 -7 -12 -7 -2 8 -19 -9 -6 -6 -9 -7 -23
+W -20 -5 -11 -21 -22 -19 -23 -21 -10 -20 -9 -18 -19 -7 -20 -8 -19 13 -8 -22 -13 -21 -16 -23
+Y -11 -14 -7 -17 -7 -18 -11 -20 -6 -9 -10 -12 -17 -1 -20 -10 -9 -8 10 -10 -9 -13 -11 -23
+V -5 -11 -12 -11 -9 -10 -10 -9 -9 -1 -5 -13 -4 -12 -9 -10 -6 -22 -10 8 -11 -10 -8 -23
+B -6 -11 7 7 -18 -6 -1 -6 -4 -9 -12 -5 -16 -14 -10 -4 -6 -13 -9 -11 7 -3 -8 -23
+Z -6 -7 -6 -1 -20 7 7 -8 -4 -9 -10 -6 -8 -20 -7 -8 -9 -21 -13 -10 -3 7 -8 -23
+X -6 -9 -6 -9 -13 -8 -8 -8 -8 -8 -9 -8 -9 -12 -8 -6 -7 -16 -11 -8 -8 -8 -8 -23
+* -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 1
diff --git a/src/jaligner/matrix/matrices/PAM100 b/src/jaligner/matrix/matrices/PAM100
new file mode 100644
index 0000000..f45c20d
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM100
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 100 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.99, Entropy = 1.18 bits
+#
+# Lowest score = -9, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -3 -1 -1 -3 -2 0 1 -3 -2 -3 -3 -2 -5 1 1 1 -7 -4 0 -1 -1 -1 -9
+R -3 7 -2 -4 -5 1 -3 -5 1 -3 -5 2 -1 -6 -1 -1 -3 1 -6 -4 -3 -1 -2 -9
+N -1 -2 5 3 -5 -1 1 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -3 4 0 -1 -9
+D -1 -4 3 5 -7 0 4 -1 -1 -4 -6 -1 -5 -8 -3 -1 -2 -9 -6 -4 4 3 -2 -9
+C -3 -5 -5 -7 9 -8 -8 -5 -4 -3 -8 -8 -7 -7 -4 -1 -4 -9 -1 -3 -6 -8 -5 -9
+Q -2 1 -1 0 -8 6 2 -3 3 -4 -2 0 -2 -7 -1 -2 -2 -7 -6 -3 0 5 -2 -9
+E 0 -3 1 4 -8 2 5 -1 -1 -3 -5 -1 -4 -8 -2 -1 -2 -9 -5 -3 3 4 -2 -9
+G 1 -5 -1 -1 -5 -3 -1 5 -4 -5 -6 -3 -4 -6 -2 0 -2 -9 -7 -3 -1 -2 -2 -9
+H -3 1 2 -1 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
+I -2 -3 -3 -4 -3 -4 -3 -5 -4 6 1 -3 1 0 -4 -3 0 -7 -3 3 -3 -3 -2 -9
+L -3 -5 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 0 -5 -4 -3 -9
+K -3 2 1 -1 -8 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -6 -6 -4 0 -1 -2 -9
+M -2 -1 -4 -5 -7 -2 -4 -4 -4 1 3 0 9 -1 -4 -3 -1 -6 -5 1 -4 -2 -2 -9
+F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -7 -1 8 -6 -4 -5 -1 4 -3 -6 -7 -4 -9
+P 1 -1 -2 -3 -4 -1 -2 -2 -1 -4 -4 -3 -4 -6 7 0 -1 -7 -7 -3 -3 -1 -2 -9
+S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -3 -4 0 4 2 -3 -4 -2 0 -2 -1 -9
+T 1 -3 0 -2 -4 -2 -2 -2 -3 0 -3 -1 -1 -5 -1 2 5 -7 -4 0 -1 -2 -1 -9
+W -7 1 -5 -9 -9 -7 -9 -9 -4 -7 -3 -6 -6 -1 -7 -3 -7 12 -2 -9 -6 -8 -6 -9
+Y -4 -6 -2 -6 -1 -6 -5 -7 -1 -3 -3 -6 -5 4 -7 -4 -4 -2 9 -4 -4 -6 -4 -9
+V 0 -4 -3 -4 -3 -3 -3 -3 -3 3 0 -4 1 -3 -3 -2 0 -9 -4 5 -4 -3 -2 -9
+B -1 -3 4 4 -6 0 3 -1 1 -3 -5 0 -4 -6 -3 0 -1 -6 -4 -4 4 2 -2 -9
+Z -1 -1 0 3 -8 5 4 -2 1 -3 -4 -1 -2 -7 -1 -2 -2 -8 -6 -3 2 5 -2 -9
+X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM110 b/src/jaligner/matrix/matrices/PAM110
new file mode 100644
index 0000000..b2b5a44
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM110
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 110 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.81, Entropy = 1.07 bits
+#
+# Lowest score = -9, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 -1 -1 -3 -1 0 1 -3 -1 -3 -3 -2 -4 1 1 1 -7 -4 0 -1 -1 -1 -9
+R -3 7 -1 -4 -4 1 -3 -4 1 -3 -4 2 -1 -5 -1 -1 -2 1 -5 -4 -2 -1 -2 -9
+N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -5 -2 -3 3 0 -1 -9
+D -1 -4 2 5 -7 1 4 0 0 -3 -6 -1 -5 -7 -3 -1 -1 -8 -5 -4 4 3 -2 -9
+C -3 -4 -5 -7 9 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 -1 -3 -9 -1 -3 -6 -7 -4 -9
+Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -6 -3 0 4 -1 -9
+E 0 -3 1 4 -7 2 5 -1 -1 -3 -5 -1 -3 -7 -2 -1 -2 -9 -5 -3 3 4 -2 -9
+G 1 -4 0 0 -5 -3 -1 5 -4 -4 -6 -3 -4 -5 -2 0 -2 -8 -7 -2 0 -2 -2 -9
+H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
+I -1 -3 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -4 -3 0 -7 -2 3 -3 -3 -2 -9
+L -3 -4 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 1 -5 -3 -2 -9
+K -3 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -5 -5 -4 0 -1 -2 -9
+M -2 -1 -3 -5 -7 -1 -3 -4 -4 1 3 0 8 -1 -4 -2 -1 -6 -5 1 -4 -2 -2 -9
+F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -6 -4 -4 -1 4 -3 -6 -7 -4 -9
+P 1 -1 -2 -3 -4 0 -2 -2 -1 -4 -4 -3 -4 -6 6 0 -1 -7 -7 -2 -2 -1 -2 -9
+S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -2 -4 0 3 2 -3 -3 -2 0 -1 -1 -9
+T 1 -2 0 -1 -3 -2 -2 -2 -3 0 -3 -1 -1 -4 -1 2 5 -6 -3 0 -1 -2 -1 -9
+W -7 1 -5 -8 -9 -6 -9 -8 -4 -7 -3 -5 -6 -1 -7 -3 -6 12 -2 -8 -6 -7 -5 -9
+Y -4 -5 -2 -5 -1 -6 -5 -7 -1 -2 -3 -5 -5 4 -7 -3 -3 -2 8 -4 -3 -5 -3 -9
+V 0 -4 -3 -4 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -4 5 -3 -3 -2 -9
+B -1 -2 3 4 -6 0 3 0 1 -3 -5 0 -4 -6 -2 0 -1 -6 -3 -3 4 2 -1 -9
+Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -7 -1 -1 -2 -7 -5 -3 2 4 -2 -9
+X -1 -2 -1 -2 -4 -1 -2 -2 -2 -2 -2 -2 -2 -4 -2 -1 -1 -5 -3 -2 -1 -2 -2 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM120 b/src/jaligner/matrix/matrices/PAM120
new file mode 100644
index 0000000..9f6a1e3
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM120
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.64, Entropy = 0.979 bits
+#
+# Lowest score = -8, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 -8
+R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
+N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 -8
+D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 -8
+C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 -8
+Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 -8
+E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 -8
+G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 -8
+H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 -8
+I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
+L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 -8
+K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 -8
+M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 -8
+F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 -8
+P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 -8
+S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
+T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
+W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 -8
+Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 -8
+V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 -8
+B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 -8
+Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
+X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM130 b/src/jaligner/matrix/matrices/PAM130
new file mode 100644
index 0000000..d2900de
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM130
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 130 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.48, Entropy = 0.895 bits
+#
+# Lowest score = -8, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
+R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
+N 0 -1 4 2 -4 0 1 0 2 -2 -3 1 -3 -4 -1 1 0 -4 -2 -3 3 0 -1 -8
+D 0 -3 2 5 -6 1 3 0 0 -3 -5 -1 -4 -7 -2 0 -1 -7 -5 -3 4 3 -1 -8
+C -3 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
+Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -6 0 -1 -2 -6 -5 -3 0 4 -1 -8
+E 0 -3 1 3 -6 2 5 -1 0 -2 -4 -1 -3 -6 -2 -1 -1 -8 -5 -3 2 4 -1 -8
+G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -4 -5 -2 1 -1 -7 -6 -2 0 -1 -2 -8
+H -2 1 2 0 -4 3 0 -3 7 -3 -3 -1 -3 -2 -1 -2 -2 -3 0 -3 1 1 -1 -8
+I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
+L -3 -4 -3 -5 -7 -2 -4 -5 -3 1 5 -4 3 1 -3 -4 -2 -2 -2 1 -4 -3 -2 -8
+K -2 2 1 -1 -6 0 -1 -3 -1 -2 -4 5 0 -6 -2 -1 0 -5 -5 -4 0 0 -1 -8
+M -2 -1 -3 -4 -6 -1 -3 -4 -3 2 3 0 8 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
+F -4 -5 -4 -7 -5 -6 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
+P 1 -1 -1 -2 -3 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -6 -6 -2 -2 -1 -1 -8
+S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
+T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
+W -6 1 -4 -7 -8 -6 -8 -7 -3 -6 -2 -5 -5 -1 -6 -2 -6 12 -1 -7 -5 -7 -5 -8
+Y -4 -5 -2 -5 -1 -5 -5 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -5 -3 -8
+V 0 -3 -3 -3 -2 -3 -3 -2 -3 3 1 -4 1 -2 -2 -2 0 -7 -3 5 -3 -3 -1 -8
+B 0 -2 3 4 -5 0 2 0 1 -3 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
+Z 0 -1 0 3 -6 4 4 -1 1 -3 -3 0 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
+X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 -1 -1 -5 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM140 b/src/jaligner/matrix/matrices/PAM140
new file mode 100644
index 0000000..5dd4dca
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM140
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 140 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.35, Entropy = 0.820 bits
+#
+# Lowest score = -8, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
+R -2 6 -1 -3 -4 1 -2 -4 1 -2 -4 3 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -1 -8
+N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -8
+D 0 -3 2 4 -6 1 3 0 0 -3 -5 -1 -4 -6 -2 0 -1 -7 -5 -3 4 3 -1 -8
+C -2 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
+Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -2 -5 -5 -2 1 4 -1 -8
+E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -3 -6 -1 -1 -1 -8 -4 -2 2 4 -1 -8
+G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -3 -5 -1 1 -1 -7 -6 -2 0 -1 -1 -8
+H -2 1 2 0 -4 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -8
+I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -2 -2 -1 -8
+L -2 -4 -3 -5 -7 -2 -4 -5 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -8
+K -2 3 1 -1 -6 0 -1 -3 -1 -2 -3 5 0 -6 -2 -1 0 -4 -5 -3 0 0 -1 -8
+M -2 -1 -2 -4 -6 -1 -3 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
+P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -6 -2 -2 -1 -1 -8
+S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 0 -8
+T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -5 -3 0 0 -1 -1 -8
+W -6 1 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 -1 -6 -2 -5 12 -1 -7 -5 -6 -5 -8
+Y -4 -5 -2 -5 -1 -5 -4 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -4 -3 -8
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -2 0 -7 -3 5 -3 -2 -1 -8
+B 0 -2 3 4 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
+Z 0 -1 1 3 -6 4 4 -1 1 -2 -3 0 -2 -6 -1 -1 -1 -6 -4 -2 2 4 -1 -8
+X -1 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -5 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM150 b/src/jaligner/matrix/matrices/PAM150
new file mode 100644
index 0000000..9b64476
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM150
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 150 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.25, Entropy = 0.754 bits
+#
+# Lowest score = -7, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -6 -3 0 0 0 -1 -7
+R -2 6 -1 -2 -4 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -2 1 -4 -3 -2 0 -1 -7
+N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -7
+D 0 -2 2 4 -6 1 3 0 0 -3 -5 -1 -3 -6 -2 0 -1 -7 -4 -3 3 2 -1 -7
+C -2 -4 -4 -6 9 -6 -6 -4 -3 -2 -6 -6 -5 -5 -3 0 -3 -7 0 -2 -5 -6 -3 -7
+Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -7
+E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -2 -6 -1 -1 -1 -7 -4 -2 2 4 -1 -7
+G 1 -3 0 0 -4 -2 -1 4 -3 -3 -4 -2 -3 -5 -1 1 -1 -7 -5 -2 0 -1 -1 -7
+H -2 1 2 0 -3 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -7
+I -1 -2 -2 -3 -2 -3 -2 -3 -3 5 1 -2 2 0 -3 -2 0 -5 -2 3 -2 -2 -1 -7
+L -2 -3 -3 -5 -6 -2 -4 -4 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
+K -2 3 1 -1 -6 0 -1 -2 -1 -2 -3 4 0 -6 -2 -1 0 -4 -4 -3 0 0 -1 -7
+M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -3 1 -3 -2 -1 -7
+F -4 -4 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -3 -1 5 -2 -5 -5 -3 -7
+P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -5 -2 -2 -1 -1 -7
+S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
+T 1 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 4 -5 -3 0 0 -1 -1 -7
+W -6 1 -4 -7 -7 -5 -7 -7 -3 -5 -2 -4 -5 -1 -6 -2 -5 12 -1 -6 -5 -6 -4 -7
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
+B 0 -2 3 3 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -2 3 2 -1 -7
+Z 0 0 1 2 -6 4 4 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 4 -1 -7
+X -1 -1 -1 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -4 -3 -1 -1 -1 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/jaligner/matrix/matrices/PAM160 b/src/jaligner/matrix/matrices/PAM160
new file mode 100644
index 0000000..e9fcd7a
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM160
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 160 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -1.14, Entropy = 0.694 bits
+#
+# Lowest score = -7, Highest score = 12
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -3 1 1 1 -5 -3 0 0 0 0 -7
+R -2 6 -1 -2 -3 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -1 1 -4 -3 -1 0 -1 -7
+N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -3 -1 1 0 -4 -2 -2 2 1 0 -7
+D 0 -2 2 4 -5 1 3 0 0 -3 -4 0 -3 -6 -2 0 -1 -6 -4 -3 3 2 -1 -7
+C -2 -3 -4 -5 9 -5 -5 -3 -3 -2 -6 -5 -5 -5 -3 0 -2 -7 0 -2 -4 -5 -3 -7
+Q -1 1 0 1 -5 5 2 -2 2 -2 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -7
+E 0 -2 1 3 -5 2 4 0 0 -2 -3 -1 -2 -5 -1 0 -1 -7 -4 -2 2 3 -1 -7
+G 1 -3 0 0 -3 -2 0 4 -3 -3 -4 -2 -3 -4 -1 1 -1 -7 -5 -2 0 -1 -1 -7
+H -2 1 2 0 -3 2 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -2 1 1 -1 -7
+I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 0 -2 -2 0 -5 -2 3 -2 -2 -1 -7
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
+K -2 3 1 0 -5 0 -1 -2 -1 -2 -3 4 0 -5 -2 -1 0 -4 -4 -3 0 0 -1 -7
+M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 0 -2 -2 -1 -4 -3 1 -3 -2 -1 -7
+F -3 -4 -3 -6 -5 -5 -5 -4 -2 0 1 -5 0 7 -4 -3 -3 -1 5 -2 -4 -5 -3 -7
+P 1 -1 -1 -2 -3 0 -1 -1 -1 -2 -3 -2 -2 -4 5 1 0 -5 -5 -2 -1 -1 -1 -7
+S 1 -1 1 0 0 -1 0 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
+T 1 -1 0 -1 -2 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -7
+W -5 1 -4 -6 -7 -5 -7 -7 -3 -5 -2 -4 -4 -1 -5 -2 -5 12 -1 -6 -5 -6 -4 -7
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
+V 0 -3 -2 -3 -2 -2 -2 -2 -2 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
+B 0 -1 2 3 -4 1 2 0 1 -2 -4 0 -3 -4 -1 0 0 -5 -3 -2 3 2 -1 -7
+Z 0 0 1 2 -5 3 3 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 3 -1 -7
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/jaligner/matrix/matrices/PAM170 b/src/jaligner/matrix/matrices/PAM170
new file mode 100644
index 0000000..5179b85
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM170
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 170 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.57, Entropy = 0.640 bits
+#
+# Lowest score = -10, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 0 0 -3 -1 0 1 -3 -1 -3 -2 -2 -5 1 2 2 -8 -5 0 0 0 -1 -10
+R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
+N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -3 -3 3 1 -1 -10
+D 0 -3 3 6 -7 2 5 0 0 -4 -6 -1 -4 -8 -2 0 -1 -9 -6 -4 5 4 -1 -10
+C -3 -5 -5 -7 13 -8 -8 -5 -5 -3 -9 -8 -7 -6 -4 0 -3 -10 0 -3 -6 -8 -4 -10
+Q -1 1 0 2 -8 6 3 -2 4 -3 -2 0 -1 -7 0 -1 -2 -7 -6 -3 1 5 -1 -10
+E 0 -2 2 5 -8 3 6 0 0 -3 -5 -1 -3 -8 -1 -1 -1 -10 -6 -3 3 5 -1 -10
+G 1 -4 0 0 -5 -2 0 6 -4 -4 -6 -3 -4 -6 -2 1 -1 -9 -7 -2 0 -1 -2 -10
+H -3 2 2 0 -5 4 0 -4 9 -4 -3 -1 -4 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
+I -1 -3 -3 -4 -3 -3 -3 -4 -4 7 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
+L -3 -4 -4 -6 -9 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -4 -2 -10
+K -2 4 1 -1 -8 0 -1 -3 -1 -3 -4 6 1 -8 -2 -1 0 -5 -6 -4 0 0 -2 -10
+M -2 -1 -3 -4 -7 -1 -3 -4 -4 2 4 1 10 0 -3 -2 -1 -6 -4 2 -4 -2 -1 -10
+F -5 -6 -5 -8 -6 -7 -8 -6 -3 1 1 -8 0 10 -6 -4 -5 -1 7 -2 -6 -7 -4 -10
+P 1 -1 -1 -2 -4 0 -1 -2 -1 -3 -4 -2 -3 -6 8 1 0 -8 -7 -2 -2 -1 -1 -10
+S 2 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
+T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -5 0 2 5 -7 -4 0 0 -1 -1 -10
+W -8 2 -5 -9 -10 -7 -10 -9 -4 -7 -3 -5 -6 -1 -8 -3 -7 18 -1 -9 -7 -8 -6 -10
+Y -5 -6 -3 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 12 -4 -4 -6 -4 -10
+V 0 -4 -3 -4 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -9 -4 6 -3 -3 -1 -10
+B 0 -2 3 5 -6 1 3 0 1 -3 -5 0 -4 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
+Z 0 0 1 4 -8 5 5 -1 2 -3 -4 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
+X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -2 -1 -4 -1 0 -1 -6 -4 -1 -1 -1 -2 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM180 b/src/jaligner/matrix/matrices/PAM180
new file mode 100644
index 0000000..2d8e07e
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM180
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 180 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.51, Entropy = 0.591 bits
+#
+# Lowest score = -10, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -8 -5 0 0 0 -1 -10
+R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
+N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -2 -3 3 1 -1 -10
+D 0 -3 3 5 -7 2 4 0 0 -3 -6 0 -4 -8 -2 0 -1 -9 -6 -3 4 3 -1 -10
+C -3 -5 -5 -7 13 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 0 -3 -10 0 -3 -6 -7 -4 -10
+Q -1 1 0 2 -7 6 3 -2 4 -3 -2 0 -1 -6 0 -1 -2 -6 -6 -3 1 5 -1 -10
+E 0 -2 2 4 -7 3 5 0 0 -3 -5 -1 -3 -7 -1 -1 -1 -9 -6 -3 3 5 -1 -10
+G 1 -4 0 0 -5 -2 0 6 -3 -4 -6 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -2 -10
+H -2 2 2 0 -4 4 0 -3 8 -4 -3 -1 -3 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
+I -1 -3 -3 -3 -3 -3 -3 -4 -4 6 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
+L -3 -4 -4 -6 -8 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -3 -2 -10
+K -2 4 1 0 -7 0 -1 -3 -1 -3 -4 6 1 -7 -2 -1 0 -5 -6 -4 0 0 -1 -10
+M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -10
+F -5 -6 -5 -8 -6 -6 -7 -6 -3 1 1 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -10
+P 1 -1 -1 -2 -4 0 -1 -1 -1 -3 -4 -2 -3 -6 8 1 0 -7 -7 -2 -2 -1 -1 -10
+S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
+T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -4 0 2 4 -7 -4 0 0 -1 -1 -10
+W -8 2 -5 -9 -10 -6 -9 -9 -4 -7 -3 -5 -6 0 -7 -3 -7 18 -1 -8 -7 -8 -6 -10
+Y -5 -6 -2 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 11 -4 -4 -6 -3 -10
+V 0 -4 -3 -3 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -8 -4 6 -3 -3 -1 -10
+B 0 -2 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
+Z 0 0 1 3 -7 5 5 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
+X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 0 -1 -6 -3 -1 -1 -1 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM190 b/src/jaligner/matrix/matrices/PAM190
new file mode 100644
index 0000000..9dd4f3a
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM190
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 190 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.35, Entropy = 0.547 bits
+#
+# Lowest score = -9, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -7 -4 0 0 0 0 -9
+R -2 8 -1 -2 -5 1 -2 -4 2 -3 -4 4 -1 -6 0 -1 -2 2 -5 -3 -1 0 -1 -9
+N 0 -1 3 3 -5 1 2 0 2 -2 -4 1 -3 -4 -1 1 0 -5 -2 -3 3 1 -1 -9
+D 0 -2 3 5 -7 2 4 0 0 -3 -5 0 -4 -7 -2 0 -1 -8 -5 -3 4 3 -1 -9
+C -3 -5 -5 -7 13 -7 -7 -4 -4 -3 -8 -7 -7 -6 -4 0 -3 -9 0 -3 -6 -7 -4 -9
+Q -1 1 1 2 -7 6 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
+E 0 -2 2 4 -7 3 5 0 0 -3 -4 -1 -3 -7 -1 0 -1 -9 -5 -3 3 4 -1 -9
+G 1 -4 0 0 -4 -2 0 6 -3 -4 -5 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -1 -9
+H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
+I -1 -3 -2 -3 -3 -3 -3 -4 -3 6 2 -3 2 1 -3 -2 0 -7 -2 4 -3 -3 -1 -9
+L -3 -4 -4 -5 -8 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -3 -2 2 -5 -3 -2 -9
+K -2 4 1 0 -7 1 -1 -3 -1 -3 -4 6 1 -7 -2 0 0 -5 -6 -3 0 0 -1 -9
+M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -9
+F -5 -6 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -9
+P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
+S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -9
+T 2 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
+W -7 2 -5 -8 -9 -6 -9 -9 -3 -7 -3 -5 -6 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
+Y -4 -5 -2 -5 0 -5 -5 -7 0 -2 -2 -6 -4 7 -6 -4 -3 -1 11 -3 -4 -5 -3 -9
+V 0 -3 -3 -3 -3 -3 -3 -2 -3 4 2 -3 2 -2 -2 -2 0 -8 -3 6 -3 -3 -1 -9
+B 0 -1 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -1 1 0 -6 -4 -3 4 2 -1 -9
+Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -7 -5 -3 2 4 -1 -9
+X 0 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM20 b/src/jaligner/matrix/matrices/PAM20
new file mode 100644
index 0000000..5ced965
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM20
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 20 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -6.18, Entropy = 2.95 bits
+#
+# Lowest score = -19, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -8 -5 -4 -8 -5 -3 -3 -8 -6 -7 -8 -6 -9 -2 -1 -1 -16 -9 -3 -5 -4 -4 -19
+R -8 9 -7 -12 -9 -2 -11 -11 -3 -6 -10 -1 -5 -10 -5 -4 -8 -3 -11 -9 -9 -5 -7 -19
+N -5 -7 8 1 -13 -5 -3 -4 -1 -6 -8 -2 -11 -10 -7 -1 -3 -9 -5 -9 6 -4 -4 -19
+D -4 -12 1 8 -16 -4 2 -4 -5 -9 -15 -6 -13 -17 -9 -5 -6 -17 -13 -9 6 0 -7 -19
+C -8 -9 -13 -16 10 -16 -16 -11 -8 -7 -17 -16 -16 -15 -9 -4 -9 -18 -5 -7 -14 -16 -11 -19
+Q -5 -2 -5 -4 -16 9 0 -8 0 -9 -6 -4 -5 -15 -4 -6 -7 -15 -14 -8 -4 7 -6 -19
+E -3 -11 -3 2 -16 0 8 -5 -6 -6 -10 -5 -8 -16 -7 -5 -7 -19 -9 -8 0 6 -6 -19
+G -3 -11 -4 -4 -11 -8 -5 7 -10 -13 -12 -8 -10 -10 -7 -3 -7 -17 -16 -7 -4 -6 -6 -19
+H -8 -3 -1 -5 -8 0 -6 -10 9 -11 -7 -8 -13 -7 -5 -7 -8 -8 -4 -7 -2 -2 -6 -19
+I -6 -6 -6 -9 -7 -9 -6 -13 -11 9 -2 -7 -2 -3 -10 -8 -3 -16 -7 1 -7 -7 -6 -19
+L -7 -10 -8 -15 -17 -6 -10 -12 -7 -2 7 -9 0 -4 -8 -9 -8 -7 -8 -3 -10 -8 -7 -19
+K -8 -1 -2 -6 -16 -4 -5 -8 -8 -7 -9 7 -3 -16 -8 -5 -4 -14 -10 -10 -3 -5 -6 -19
+M -6 -5 -11 -13 -16 -5 -8 -10 -13 -2 0 -3 11 -5 -9 -6 -5 -15 -13 -2 -12 -6 -6 -19
+F -9 -10 -10 -17 -15 -15 -16 -10 -7 -3 -4 -16 -5 9 -11 -7 -10 -6 1 -9 -12 -16 -9 -19
+P -2 -5 -7 -9 -9 -4 -7 -7 -5 -10 -8 -8 -9 -11 8 -3 -5 -16 -16 -7 -8 -5 -6 -19
+S -1 -4 -1 -5 -4 -6 -5 -3 -7 -8 -9 -5 -6 -7 -3 7 0 -6 -8 -8 -2 -6 -4 -19
+T -1 -8 -3 -6 -9 -7 -7 -7 -8 -3 -8 -4 -5 -10 -5 0 7 -15 -7 -4 -4 -7 -5 -19
+W -16 -3 -9 -17 -18 -15 -19 -17 -8 -16 -7 -14 -15 -6 -16 -6 -15 13 -6 -18 -11 -17 -13 -19
+Y -9 -11 -5 -13 -5 -14 -9 -16 -4 -7 -8 -10 -13 1 -16 -8 -7 -6 10 -8 -7 -11 -9 -19
+V -3 -9 -9 -9 -7 -8 -8 -7 -7 1 -3 -10 -2 -9 -7 -8 -4 -18 -8 7 -9 -8 -6 -19
+B -5 -9 6 6 -14 -4 0 -4 -2 -7 -10 -3 -12 -12 -8 -2 -4 -11 -7 -9 6 -1 -6 -19
+Z -4 -5 -4 0 -16 7 6 -6 -2 -7 -8 -5 -6 -16 -5 -6 -7 -17 -11 -8 -1 6 -6 -19
+X -4 -7 -4 -7 -11 -6 -6 -6 -6 -6 -7 -6 -6 -9 -6 -4 -5 -13 -9 -6 -6 -6 -6 -19
+* -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 1
diff --git a/src/jaligner/matrix/matrices/PAM200 b/src/jaligner/matrix/matrices/PAM200
new file mode 100644
index 0000000..cb46b37
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM200
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 200 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.23, Entropy = 0.507 bits
+#
+# Lowest score = -9, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 3 -2 0 0 -3 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -2 -4 1 -2 -4 2 -2 -4 4 -1 -5 0 -1 -1 2 -5 -3 -1 0 -1 -9
+N 0 0 3 3 -5 1 2 0 2 -2 -4 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
+D 0 -2 3 5 -6 2 4 0 0 -3 -5 0 -4 -7 -2 0 0 -8 -5 -3 4 3 -1 -9
+C -3 -4 -5 -6 12 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -9 0 -2 -5 -7 -4 -9
+Q -1 1 1 2 -7 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
+E 0 -2 2 4 -7 3 5 0 0 -3 -4 0 -3 -7 -1 0 -1 -9 -5 -2 3 4 -1 -9
+G 1 -4 0 0 -4 -2 0 6 -3 -3 -5 -2 -4 -6 -1 1 0 -8 -6 -2 0 -1 -1 -9
+H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
+I -1 -2 -2 -3 -3 -3 -3 -3 -3 6 2 -2 2 1 -3 -2 0 -6 -2 4 -3 -3 -1 -9
+L -2 -4 -4 -5 -7 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -2 -2 2 -4 -3 -2 -9
+K -2 4 1 0 -7 1 0 -2 -1 -2 -4 6 1 -7 -2 0 0 -4 -5 -3 0 0 -1 -9
+M -2 -1 -2 -4 -6 -1 -3 -4 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
+F -4 -5 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -6 -3 -9
+P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
+S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 2 2 -3 -3 -1 1 -1 0 -9
+T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
+W -7 2 -5 -8 -9 -6 -9 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
+Y -4 -5 -2 -5 0 -5 -5 -6 0 -2 -2 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
+V 0 -3 -2 -3 -2 -3 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -8 -3 5 -3 -2 -1 -9
+B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -6 -1 1 0 -6 -4 -3 3 2 -1 -9
+Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -6 -1 -1 -1 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM210 b/src/jaligner/matrix/matrices/PAM210
new file mode 100644
index 0000000..0d485c9
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM210
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 210 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.12, Entropy = 0.470 bits
+#
+# Lowest score = -9, Highest score = 18
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -2 -4 1 -2 -3 2 -2 -4 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -9
+N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
+D 0 -2 2 5 -6 2 4 0 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -9
+C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 0 -2 -5 -6 -4 -9
+Q -1 1 1 2 -6 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -2 1 4 -1 -9
+E 0 -2 2 4 -6 3 5 0 0 -2 -4 0 -3 -6 -1 0 -1 -8 -5 -2 3 4 -1 -9
+G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -9
+H -2 2 2 1 -4 3 0 -3 8 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -9
+I -1 -2 -2 -3 -3 -3 -2 -3 -3 5 2 -2 2 1 -3 -2 0 -6 -1 4 -3 -3 -1 -9
+L -2 -4 -3 -5 -7 -2 -4 -5 -2 2 7 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -9
+K -2 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -2 0 0 -4 -5 -3 0 0 -1 -9
+M -1 -1 -2 -3 -6 -1 -3 -3 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
+F -4 -5 -4 -7 -5 -6 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -9
+P 1 0 -1 -1 -3 0 -1 -1 0 -3 -3 -2 -3 -5 7 1 0 -7 -6 -2 -1 0 -1 -9
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 1 0 0 -9
+T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -9
+W -7 2 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -7 -6 -7 -5 -9
+Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -7 -3 5 -2 -2 -1 -9
+B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
+Z 0 0 1 3 -6 4 4 -1 2 -3 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM220 b/src/jaligner/matrix/matrices/PAM220
new file mode 100644
index 0000000..fcaaecf
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM220
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 220 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -1.06, Entropy = 0.437 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
+N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -2 2 4 -6 2 4 0 1 -3 -5 0 -3 -6 -1 0 0 -8 -5 -3 4 3 -1 -8
+C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 0 -2 -5 -6 -3 -8
+Q -1 1 1 2 -6 5 3 -2 3 -2 -2 1 -1 -5 0 -1 -1 -5 -5 -2 1 4 -1 -8
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
+G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -8
+H -2 2 2 1 -4 3 1 -3 7 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -8
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -5 -7 -2 -4 -5 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -1 0 0 -4 -5 -3 0 0 -1 -8
+M -1 -1 -2 -3 -6 -1 -2 -3 -3 2 4 1 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 7 1 0 -6 -6 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 0 0 0 -8
+T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -8
+W -6 2 -4 -8 -8 -5 -8 -8 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -7 -5 -8
+Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 0 11 -3 -3 -5 -3 -8
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -1 -1 0 -7 -3 5 -2 -2 -1 -8
+B 0 -1 2 4 -5 1 3 0 1 -2 -4 0 -3 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM230 b/src/jaligner/matrix/matrices/PAM230
new file mode 100644
index 0000000..4ecddbe
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM230
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 230 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.991, Entropy = 0.407 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -2 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -8
+C -2 -4 -4 -6 12 -6 -6 -4 -4 -2 -7 -6 -6 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
+Q -1 1 1 2 -6 5 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -8
+E 0 -1 1 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
+G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -6 -2 0 -1 -1 -8
+H -2 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -2 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -8
+M -1 -1 -2 -3 -6 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 9 -5 -3 -3 0 7 -1 -5 -6 -3 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -3 1 2 2 -3 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 -1 0 -2 0 -2 0 -1 -3 0 2 3 -6 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -6 -4 -8
+Y -4 -5 -2 -5 0 -4 -5 -6 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -5 -3 -8
+V 0 -3 -2 -2 -2 -2 -2 -2 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -8
+B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -6 -5 -2 2 4 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM240 b/src/jaligner/matrix/matrices/PAM240
new file mode 100644
index 0000000..ce19219
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM240
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 240 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.923, Entropy = 0.379 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -5 0 0 -1 2 -4 -3 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
+D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+C -2 -4 -4 -5 12 -6 -6 -4 -4 -2 -6 -6 -5 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
+Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
+E 0 -1 1 4 -6 3 4 0 1 -2 -3 0 -2 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
+H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -8
+K -1 3 1 0 -6 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -4 -5 -3 1 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -4 -3 2 -2 -2 -1 -8
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -5 -5 -2 -8
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -3 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -4 -4 0 -6 -3 -5 17 0 -6 -5 -6 -4 -8
+Y -4 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -4 -2 -8
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -6 -3 4 -2 -2 -1 -8
+B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -5 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -6 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM250 b/src/jaligner/matrix/matrices/PAM250
new file mode 100644
index 0000000..bdbb2a7
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM250
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.844, Entropy = 0.354 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
+G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
+F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
+P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
+B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM260 b/src/jaligner/matrix/matrices/PAM260
new file mode 100644
index 0000000..df46c1b
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM260
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 260 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.794, Entropy = 0.330 bits
+#
+# Lowest score = -7, Highest score = 17
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -7
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -7
+N 0 0 2 2 -3 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -7
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -5 -1 0 0 -6 -4 -2 3 3 -1 -7
+C -2 -4 -3 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -7 0 -2 -4 -5 -3 -7
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -4 0 0 -1 -5 -4 -2 1 3 0 -7
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 3 3 -1 -7
+G 1 -2 0 1 -3 -1 0 5 -2 -2 -4 -2 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -7
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -7
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -7
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -2 -3 -2 -2 -1 2 -3 -2 -1 -7
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -7
+M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -1 -1 -4 -2 2 -2 -2 -1 -7
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 2 -5 0 9 -4 -3 -3 0 7 -1 -4 -5 -2 -7
+P 1 0 0 -1 -3 0 0 0 0 -2 -2 -1 -2 -4 6 1 0 -5 -5 -1 -1 0 -1 -7
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -2 -3 -1 0 0 0 -7
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 2 -5 -3 0 0 0 0 -7
+W -6 2 -4 -6 -7 -5 -7 -7 -3 -5 -2 -3 -4 0 -5 -2 -5 17 0 -6 -5 -6 -4 -7
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -7
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -7
+B 0 -1 2 3 -4 1 3 1 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 0 -7
+Z 0 0 1 3 -5 3 3 0 2 -2 -2 0 -2 -5 0 0 0 -6 -4 -2 2 3 -1 -7
+X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 0 -1 -1 -7
+* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/src/jaligner/matrix/matrices/PAM270 b/src/jaligner/matrix/matrices/PAM270
new file mode 100644
index 0000000..afd53be
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM270
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 270 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.969, Entropy = 0.309 bits
+#
+# Lowest score = -10, Highest score = 23
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 2 -2 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -10
+R -2 8 0 -1 -5 2 -1 -3 2 -2 -4 4 -1 -5 0 0 -1 3 -5 -3 -1 0 -1 -10
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
+D 0 -1 2 5 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -10
+C -2 -5 -4 -6 16 -7 -6 -4 -4 -3 -7 -7 -6 -5 -3 0 -3 -10 1 -2 -5 -7 -4 -10
+Q 0 2 1 2 -7 5 3 -1 4 -2 -2 1 -1 -6 0 -1 -1 -6 -5 -2 2 4 -1 -10
+E 0 -1 2 4 -6 3 5 0 1 -2 -4 0 -3 -7 -1 0 0 -9 -5 -2 3 4 -1 -10
+G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -9 -6 -2 1 0 -1 -10
+H -2 2 2 1 -4 4 1 -2 8 -3 -3 0 -3 -2 0 -1 -1 -3 0 -3 1 2 -1 -10
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 5 -3 -2 -1 -10
+L -2 -4 -3 -5 -7 -2 -4 -5 -3 3 8 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -10
+K -1 4 1 0 -7 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -10
+M -1 -1 -2 -3 -6 -1 -3 -3 -3 3 5 0 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -10
+F -4 -5 -4 -7 -5 -6 -7 -6 -2 1 2 -6 0 12 -6 -4 -4 1 9 -1 -6 -6 -3 -10
+P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -6 7 1 0 -7 -6 -1 -1 0 -1 -10
+S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -4 -1 1 0 0 -10
+T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -10
+W -7 3 -5 -8 -10 -6 -9 -9 -3 -6 -2 -4 -5 1 -7 -3 -6 23 0 -8 -7 -7 -5 -10
+Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -4 -3 0 13 -3 -4 -5 -3 -10
+V 0 -3 -2 -3 -2 -2 -2 -2 -3 5 2 -3 2 -1 -1 -1 0 -8 -3 5 -2 -2 -1 -10
+B 0 -1 2 4 -5 2 3 1 1 -3 -4 1 -3 -6 -1 1 0 -7 -4 -2 3 3 -1 -10
+Z 0 0 2 3 -7 4 4 0 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 3 4 -1 -10
+X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM280 b/src/jaligner/matrix/matrices/PAM280
new file mode 100644
index 0000000..1662747
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM280
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 280 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.916, Entropy = 0.289 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 -1 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
+D 0 -1 2 4 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -2 4 3 -1 -9
+C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -6 -5 -2 2 4 -1 -9
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
+G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 8 -3 -2 0 -2 -2 0 -1 -1 -3 0 -3 1 2 -1 -9
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -5 -7 -2 -4 -5 -2 3 7 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -9
+F -4 -5 -4 -7 -5 -5 -6 -6 -2 1 2 -6 0 11 -5 -4 -4 1 9 -1 -5 -6 -3 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -7 -6 -1 -1 0 -1 -9
+S 1 0 1 0 0 0 0 1 -1 -2 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
+T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 1 1 3 -6 -3 0 0 0 0 -9
+W -7 3 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 22 0 -7 -6 -7 -5 -9
+Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -3 -3 0 13 -3 -4 -5 -3 -9
+V 0 -3 -2 -2 -2 -2 -2 -1 -3 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
+B 0 -1 2 4 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
+Z 0 0 1 3 -6 4 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM290 b/src/jaligner/matrix/matrices/PAM290
new file mode 100644
index 0000000..7c139e8
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM290
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 290 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.877, Entropy = 0.271 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
+R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
+D 0 -1 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -8 -5 -2 3 3 -1 -9
+C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -5 -2 2 3 0 -9
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
+G 2 -3 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -9
+I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
+F -4 -5 -4 -6 -5 -5 -6 -6 -2 1 3 -6 0 11 -5 -4 -3 1 9 -1 -5 -6 -3 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -6 -6 -1 -1 0 -1 -9
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
+T 1 -1 1 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 3 -6 -3 0 0 0 0 -9
+W -7 3 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -7 -5 -9
+Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -2 9 -6 -3 -3 0 13 -3 -4 -5 -2 -9
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
+B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 0 -9
+Z 0 0 1 3 -6 3 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
+X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -2 -1 0 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM30 b/src/jaligner/matrix/matrices/PAM30
new file mode 100644
index 0000000..32202e1
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM30
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -5.06, Entropy = 2.57 bits
+#
+# Lowest score = -17, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
+R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
+N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
+D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
+C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
+Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
+E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
+G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
+H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
+I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
+L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
+K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
+M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
+F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
+P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
+S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
+T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
+W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
+Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
+V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
+B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
+Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
+X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17
+* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
diff --git a/src/jaligner/matrix/matrices/PAM300 b/src/jaligner/matrix/matrices/PAM300
new file mode 100644
index 0000000..df49f47
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM300
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 300 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.835, Entropy = 0.254 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 0 -2 0 0 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
+R -1 7 0 -1 -4 2 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -2 -2 2 1 0 -9
+D 0 -1 2 4 -6 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
+C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
+E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 -1 -9
+G 2 -2 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -3 -2 -2 -3 -2 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -4 -3 -1 -9
+K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
+F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 3 -6 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 -1 -9
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -6 3 -5 -7 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
+Y -4 -5 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -3 -4 -5 -2 -9
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -3 5 -2 -2 0 -9
+B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
+Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 -1 -9
+X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 -1 0 0 -4 -2 0 0 -1 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM310 b/src/jaligner/matrix/matrices/PAM310
new file mode 100644
index 0000000..03025eb
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM310
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 310 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.779, Entropy = 0.238 bits
+#
+# Lowest score = -9, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -9
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -9
+D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -2 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
+C -2 -4 -4 -5 15 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
+E 0 -1 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -9
+G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 1 -2 -1 0 -5 -1 4 -2 -2 -1 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -3 -3 -1 -9
+K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -9
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 -1 -9
+F -4 -5 -4 -6 -4 -5 -6 -5 -2 1 3 -5 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
+P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -6 3 -4 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
+Y -4 -4 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -2 -4 -4 -2 -9
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
+B 0 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
+Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -9
+X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM320 b/src/jaligner/matrix/matrices/PAM320
new file mode 100644
index 0000000..5c4a568
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM320
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 320 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.741, Entropy = 0.224 bits
+#
+# Lowest score = -8, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -8
+N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -8
+D 1 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -8
+C -2 -4 -4 -5 15 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 0 0 -5 -4 -2 2 3 0 -8
+E 0 -1 2 3 -5 2 4 1 1 -2 -3 0 -2 -5 0 0 0 -7 -5 -2 3 3 0 -8
+G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -8
+H -1 2 2 1 -4 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 0 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -2 -2 0 2 -3 -3 -1 -8
+K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -8
+M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 1 -2 -1 -1 -4 -2 2 -2 -2 0 -8
+F -4 -5 -4 -6 -4 -5 -5 -5 -2 1 3 -5 1 11 -5 -3 -3 1 9 -1 -5 -5 -2 -8
+P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 -1 0 0 -2 0 0 0 -1 0 -2 0 -1 -3 1 1 2 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -6 -6 -4 -8
+Y -4 -4 -2 -5 1 -4 -5 -5 0 -1 0 -5 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
+B 0 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -3 -2 2 2 0 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -8
+X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM330 b/src/jaligner/matrix/matrices/PAM330
new file mode 100644
index 0000000..51f0d1e
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM330
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 330 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.693, Entropy = 0.210 bits
+#
+# Lowest score = -8, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
+R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -4 0 0 -1 3 -4 -2 0 0 -1 -8
+N 0 0 2 2 -4 1 2 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
+D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
+C -2 -4 -4 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
+E 0 -1 2 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 2 3 0 -8
+G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
+H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 4 -2 -2 0 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -3 -1 -2 0 2 -3 -2 -1 -8
+K -1 4 1 0 -5 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 1 -1 -8
+M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -5 -3 -3 1 9 -1 -4 -5 -2 -8
+P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
+S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 -1 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
+B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM340 b/src/jaligner/matrix/matrices/PAM340
new file mode 100644
index 0000000..cdbec3f
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM340
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 340 substitution matrix, scale = ln(2)/4 = 0.173287
+#
+# Expected score = -0.680, Entropy = 0.198 bits
+#
+# Lowest score = -8, Highest score = 22
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
+R -1 6 0 -1 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 0 -1 -8
+N 0 0 1 2 -3 1 1 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
+D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
+C -2 -4 -3 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
+E 0 0 1 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
+G 1 -2 1 1 -3 -1 1 4 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
+H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 0 -1 -2 0 -2 1 2 0 -8
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 3 -2 -2 0 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -2 -1 -2 0 2 -3 -2 -1 -8
+K -1 4 1 0 -5 1 0 -1 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 1 0 -8
+M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -4 -3 -3 1 9 -1 -4 -5 -2 -8
+P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -4 5 1 1 -5 -5 -1 0 0 0 -8
+S 1 0 1 0 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 0 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 1 -5 -3 -5 22 1 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
+V 0 -2 -1 -2 -2 -2 -1 -1 -2 3 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
+B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM350 b/src/jaligner/matrix/matrices/PAM350
new file mode 100644
index 0000000..3490108
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM350
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 350 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.701, Entropy = 0.186 bits
+#
+# Lowest score = -10, Highest score = 27
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 2 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 7 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 -1 4 -5 -3 0 1 -1 -10
+N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
+D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -3 -6 0 1 0 -8 -5 -2 3 3 -1 -10
+C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -10 1 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -5 -2 2 3 0 -10
+E 1 0 2 4 -6 3 4 1 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -10
+G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -10
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 5 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
+L -2 -3 -3 -4 -7 -2 -4 -4 -2 4 8 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -10
+K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -10
+M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 0 -10
+F -4 -5 -4 -6 -5 -5 -6 -6 -2 2 3 -6 1 13 -5 -4 -3 1 11 -1 -5 -6 -2 -10
+P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -7 -6 -1 0 0 0 -10
+S 1 0 1 1 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 -1 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 27 1 -7 -6 -7 -5 -10
+Y -4 -5 -3 -5 1 -5 -5 -6 0 0 0 -5 -2 11 -6 -3 -3 1 14 -2 -4 -5 -2 -10
+V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 5 -2 -2 0 -10
+B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -10
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 3 0 -10
+X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -5 -2 0 0 0 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM360 b/src/jaligner/matrix/matrices/PAM360
new file mode 100644
index 0000000..f316fe0
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM360
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 360 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.697, Entropy = 0.175 bits
+#
+# Lowest score = -9, Highest score = 27
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
+R -1 6 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 -1 -9
+N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -9
+D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -9
+C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 3 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
+E 1 0 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
+G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -7 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -9
+K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 0 -9
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 3 -6 1 12 -5 -4 -3 2 11 -1 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -7 4 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -4 2 -6 -3 -6 27 1 -7 -6 -7 -4 -9
+Y -4 -5 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
+B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -9
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM370 b/src/jaligner/matrix/matrices/PAM370
new file mode 100644
index 0000000..8128be6
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM370
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 370 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.649, Entropy = 0.165 bits
+#
+# Lowest score = -9, Highest score = 27
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 -1 -9
+N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 4 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 18 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
+Q 0 2 1 2 -6 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
+E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
+G 2 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 1 -8 -6 -1 1 0 -1 -9
+H -1 2 2 1 -4 3 1 -2 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -1 -2 0 3 -3 -3 -1 -9
+K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 -1 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -9
+F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 3 -6 1 12 -5 -4 -3 2 11 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -7 3 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 27 1 -7 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -9
+B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 0 -9
+X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM380 b/src/jaligner/matrix/matrices/PAM380
new file mode 100644
index 0000000..a4d7e83
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM380
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 380 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.612, Entropy = 0.156 bits
+#
+# Lowest score = -9, Highest score = 26
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 2 1 2 -5 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 3 3 0 -9
+G 2 -2 1 1 -3 -1 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -1 -2 0 3 -3 -3 -1 -9
+K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -9
+F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 3 -5 1 12 -5 -4 -3 2 10 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
+W -6 3 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 26 1 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -2 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -2 0 -9
+B 1 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM390 b/src/jaligner/matrix/matrices/PAM390
new file mode 100644
index 0000000..8e9d14c
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM390
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 390 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.581, Entropy = 0.147 bits
+#
+# Lowest score = -9, Highest score = 26
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
+R -1 6 1 0 -4 1 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -4 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 3 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -1 2 3 0 -9
+G 1 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -9
+K -1 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 3 -5 1 12 -5 -3 -3 2 10 0 -5 -5 -2 -9
+P 1 0 0 0 -3 0 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
+W -6 3 -4 -7 -9 -5 -7 -7 -3 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -1 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -1 0 -9
+B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
+Z 0 1 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM40 b/src/jaligner/matrix/matrices/PAM40
new file mode 100644
index 0000000..86ff854
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM40
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -4.27, Entropy = 2.26 bits
+#
+# Lowest score = -15, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2 -3 -2 -3 -15
+R -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7 -6 -3 -5 -15
+N -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7 6 -2 -3 -15
+D -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7 6 2 -5 -15
+C -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5 -11 -12 -8 -15
+Q -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6 -2 6 -4 -15
+E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6 2 6 -4 -15
+G -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5 -2 -4 -4 -15
+H -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6 -1 0 -4 -15
+I -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2 -5 -5 -4 -15
+L -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2 -8 -6 -5 -15
+K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8 -2 -3 -4 -15
+M -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1 -8 -4 -4 -15
+F -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7 -9 -12 -7 -15
+P -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5 -6 -3 -4 -15
+S 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5 -1 -4 -2 -15
+T 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2 -2 -5 -3 -15
+W -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14 -9 -13 -9 -15
+Y -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6 -6 -8 -7 -15
+V -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7 -7 -6 -4 -15
+B -3 -6 6 6 -11 -2 2 -2 -1 -5 -8 -2 -8 -9 -6 -1 -2 -9 -6 -7 6 1 -4 -15
+Z -2 -3 -2 2 -12 6 6 -4 0 -5 -6 -3 -4 -12 -3 -4 -5 -13 -8 -6 1 6 -4 -15
+X -3 -5 -3 -5 -8 -4 -4 -4 -4 -4 -5 -4 -4 -7 -4 -2 -3 -9 -7 -4 -4 -4 -4 -15
+* -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 1
diff --git a/src/jaligner/matrix/matrices/PAM400 b/src/jaligner/matrix/matrices/PAM400
new file mode 100644
index 0000000..4945a6c
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM400
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 400 substitution matrix, scale = ln(2)/5 = 0.138629
+#
+# Expected score = -0.521, Entropy = 0.139 bits
+#
+# Lowest score = -8, Highest score = 26
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 1 0 0 -8
+R -1 5 1 0 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 1 0 -8
+N 0 1 1 2 -3 1 2 1 1 -1 -3 1 -1 -3 0 1 0 -4 -3 -1 2 1 0 -8
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -2 2 2 0 -8
+C -2 -4 -3 -5 17 -5 -5 -3 -3 -2 -6 -5 -5 -4 -2 0 -2 -8 1 -2 -4 -5 -3 -8
+Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 2 0 -8
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
+G 1 -2 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -8
+H -1 2 1 1 -3 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -8
+I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -8
+L -2 -3 -3 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -8
+K -1 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -8
+M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 5 1 -1 -1 0 -4 -1 2 -2 -1 0 -8
+F -3 -4 -3 -5 -4 -4 -5 -5 -2 2 3 -5 1 11 -4 -3 -3 2 10 0 -4 -5 -2 -8
+P 1 0 0 0 -2 0 0 0 0 -1 -2 0 -1 -4 5 1 1 -6 -5 -1 0 0 0 -8
+S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -8
+W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -5 -6 -4 -8
+Y -3 -4 -3 -4 1 -4 -4 -5 0 0 0 -4 -1 10 -5 -3 -3 1 13 -2 -3 -4 -2 -8
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -8
+B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 2 0 -8
+Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -8
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/src/jaligner/matrix/matrices/PAM410 b/src/jaligner/matrix/matrices/PAM410
new file mode 100644
index 0000000..c2e10fa
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM410
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 410 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.617, Entropy = 0.131 bits
+#
+# Lowest score = -10, Highest score = 31
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 1 -5 -3 -1 2 2 0 -10
+D 1 0 2 3 -6 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+C -2 -4 -4 -6 20 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
+E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+G 2 -2 1 1 -4 0 1 5 -1 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 0 -10
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
+L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 8 -3 5 4 -3 -3 -1 -2 1 3 -3 -3 -1 -10
+K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -10
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 14 -5 -4 -3 2 12 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 0 0 -2 -3 0 -2 -5 6 1 1 -7 -5 -1 0 0 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 0 1 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -7 -3 -6 31 2 -7 -6 -7 -4 -10
+Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -2 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
+B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM420 b/src/jaligner/matrix/matrices/PAM420
new file mode 100644
index 0000000..daffa1a
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM420
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 420 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.599, Entropy = 0.124 bits
+#
+# Lowest score = -10, Highest score = 31
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 2 0 -10
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+C -2 -4 -4 -5 20 -6 -6 -3 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
+E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 0 1 1 -8 -6 -1 1 0 0 -10
+H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
+L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 7 -3 5 4 -2 -3 -1 -2 1 3 -3 -3 -1 -10
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -1 -2 -6 -1 -2 -2 -2 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -10
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -7 -4 -10
+Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
+V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
+B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
+Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -7 -5 -2 2 3 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM430 b/src/jaligner/matrix/matrices/PAM430
new file mode 100644
index 0000000..a7e4ace
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM430
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 430 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.543, Entropy = 0.117 bits
+#
+# Lowest score = -9, Highest score = 31
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
+R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
+C -2 -4 -4 -5 20 -6 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 3 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -9
+G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -9
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
+F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -7 4 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -9
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -9
+B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -5 -1 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM440 b/src/jaligner/matrix/matrices/PAM440
new file mode 100644
index 0000000..31645b6
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM440
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 440 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.529, Entropy = 0.111 bits
+#
+# Lowest score = -9, Highest score = 30
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -2 2 2 0 -9
+C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
+Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
+G 2 -2 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -4 -5 -4 -6 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 30 2 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -4 -2 -9
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -9
+B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM450 b/src/jaligner/matrix/matrices/PAM450
new file mode 100644
index 0000000..890c0ed
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM450
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 450 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.476, Entropy = 0.105 bits
+#
+# Lowest score = -9, Highest score = 30
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 -1 0 -2 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -4 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -2 0 -2 -9 1 -2 -4 -5 -2 -9
+Q 0 2 1 2 -5 3 2 0 3 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
+G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -2 -3 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -4 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -3 -3 2 12 0 -4 -5 -2 -9
+P 1 0 0 0 -2 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
+W -6 4 -4 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 14 -2 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
+B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM460 b/src/jaligner/matrix/matrices/PAM460
new file mode 100644
index 0000000..f1d4e6b
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM460
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 460 substitution matrix, scale = ln(2)/6 = 0.115525
+#
+# Expected score = -0.429, Entropy = 0.0994 bits
+#
+# Lowest score = -9, Highest score = 30
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
+R -1 5 1 0 -4 1 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -3 0 1 0 -4 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
+C -2 -4 -3 -5 19 -5 -5 -3 -3 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
+Q 0 1 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 1 2 0 -9
+E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
+G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -7 -5 -1 1 0 0 -9
+H 0 2 1 1 -3 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -1 -2 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -4 -3 -5 -3 -4 -5 -5 -2 2 3 -5 1 12 -4 -3 -3 2 11 0 -4 -5 -2 -9
+P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 0 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
+W -6 4 -4 -7 -9 -5 -7 -7 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
+Y -3 -4 -3 -4 2 -4 -4 -5 0 0 1 -4 -1 11 -5 -3 -3 2 14 -2 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
+B 1 0 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 2 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM470 b/src/jaligner/matrix/matrices/PAM470
new file mode 100644
index 0000000..df44357
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM470
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 470 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.520, Entropy = 0.0942 bits
+#
+# Lowest score = -10, Highest score = 35
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 1 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 6 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
+N 1 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
+D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
+C -2 -4 -4 -5 22 -6 -5 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -10 2 -2 -5 -6 -3 -10
+Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -10
+G 2 -1 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 1 1 1 -8 -6 -1 1 1 0 -10
+H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
+I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 8 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -1 -2 -6 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
+F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -4 -3 -1 1 0 0 -10
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
+W -7 4 -5 -8 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -4 -6 35 2 -7 -6 -7 -4 -10
+Y -4 -5 -3 -5 2 -4 -5 -6 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
+V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -10
+B 1 0 2 3 -5 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
+Z 0 1 1 3 -6 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -7 -5 -1 2 3 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM480 b/src/jaligner/matrix/matrices/PAM480
new file mode 100644
index 0000000..8c17f62
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM480
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 480 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.494, Entropy = 0.0893 bits
+#
+# Lowest score = -10, Highest score = 35
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 1 1 -2 0 1 2 0 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
+R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -10
+N 1 1 1 2 -4 1 2 1 1 -1 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -1 2 2 0 -10
+C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -10 2 -2 -4 -5 -3 -10
+Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -8 -5 -1 2 3 0 -10
+G 2 -1 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -10
+H 0 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
+I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
+L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
+K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
+F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
+P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
+W -7 4 -5 -7 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -3 -6 35 2 -7 -6 -6 -4 -10
+Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 3 -1 -1 0 -10
+B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
+Z 0 1 1 2 -5 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -6 -5 -1 2 2 0 -10
+X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/matrices/PAM490 b/src/jaligner/matrix/matrices/PAM490
new file mode 100644
index 0000000..b194d1f
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM490
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 490 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.431, Entropy = 0.0847 bits
+#
+# Lowest score = -9, Highest score = 34
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 2 0 0 -1 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 2 -2 -4 -5 -2 -9
+Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+G 2 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
+H 0 2 1 1 -4 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -1 -3 -2 -3 -6 -2 -3 -3 -2 4 7 -2 5 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
+F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -9
+P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 4 1 1 -6 -5 -1 0 1 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
+Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -2 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
+B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM50 b/src/jaligner/matrix/matrices/PAM50
new file mode 100644
index 0000000..75aa4fb
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM50
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 50 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -3.70, Entropy = 2.00 bits
+#
+# Lowest score = -13, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -5 -2 -2 -5 -3 -1 -1 -5 -3 -5 -5 -4 -7 0 0 0 -11 -6 -1 -2 -2 -2 -13
+R -5 8 -4 -7 -6 0 -7 -7 0 -4 -7 1 -3 -8 -3 -2 -5 -1 -8 -6 -5 -2 -4 -13
+N -2 -4 7 2 -8 -2 -1 -2 1 -4 -6 0 -6 -7 -4 1 -1 -7 -3 -6 5 -1 -2 -13
+D -2 -7 2 7 -11 -1 3 -2 -2 -6 -10 -3 -8 -12 -6 -2 -3 -12 -9 -6 6 2 -4 -13
+C -5 -6 -8 -11 9 -11 -11 -7 -6 -5 -12 -11 -11 -10 -6 -2 -6 -13 -3 -5 -9 -11 -7 -13
+Q -3 0 -2 -1 -11 8 2 -5 2 -6 -4 -2 -3 -10 -2 -4 -4 -10 -9 -5 -2 6 -3 -13
+E -1 -7 -1 3 -11 2 7 -3 -3 -4 -7 -3 -5 -11 -4 -3 -4 -13 -7 -5 2 6 -3 -13
+G -1 -7 -2 -2 -7 -5 -3 6 -7 -8 -9 -6 -7 -8 -4 -1 -4 -12 -11 -4 -2 -4 -4 -13
+H -5 0 1 -2 -6 2 -3 -7 9 -7 -5 -4 -8 -5 -3 -4 -5 -6 -2 -5 0 0 -4 -13
+I -3 -4 -4 -6 -5 -6 -4 -8 -7 8 0 -5 0 -1 -7 -5 -1 -11 -5 3 -5 -5 -3 -13
+L -5 -7 -6 -10 -12 -4 -7 -9 -5 0 6 -6 2 -1 -6 -7 -5 -5 -5 -1 -7 -5 -5 -13
+K -5 1 0 -3 -11 -2 -3 -6 -4 -5 -6 6 -1 -11 -5 -3 -2 -9 -8 -7 -1 -2 -4 -13
+M -4 -3 -6 -8 -11 -3 -5 -7 -8 0 2 -1 10 -3 -6 -4 -3 -10 -8 0 -7 -4 -4 -13
+F -7 -8 -7 -12 -10 -10 -11 -8 -5 -1 -1 -11 -3 9 -8 -5 -7 -3 3 -6 -9 -11 -6 -13
+P 0 -3 -4 -6 -6 -2 -4 -4 -3 -7 -6 -5 -6 -8 8 -1 -3 -11 -11 -4 -5 -3 -4 -13
+S 0 -2 1 -2 -2 -4 -3 -1 -4 -5 -7 -3 -4 -5 -1 6 1 -4 -5 -4 -1 -3 -2 -13
+T 0 -5 -1 -3 -6 -4 -4 -4 -5 -1 -5 -2 -3 -7 -3 1 6 -10 -5 -2 -2 -4 -2 -13
+W -11 -1 -7 -12 -13 -10 -13 -12 -6 -11 -5 -9 -10 -3 -11 -4 -10 13 -4 -12 -8 -11 -9 -13
+Y -6 -8 -3 -9 -3 -9 -7 -11 -2 -5 -5 -8 -8 3 -11 -5 -5 -4 9 -6 -5 -8 -6 -13
+V -1 -6 -6 -6 -5 -5 -5 -4 -5 3 -1 -7 0 -6 -4 -4 -2 -12 -6 7 -6 -5 -3 -13
+B -2 -5 5 6 -9 -2 2 -2 0 -5 -7 -1 -7 -9 -5 -1 -2 -8 -5 -6 5 1 -3 -13
+Z -2 -2 -1 2 -11 6 6 -4 0 -5 -5 -2 -4 -11 -3 -3 -4 -11 -8 -5 1 6 -3 -13
+X -2 -4 -2 -4 -7 -3 -3 -4 -4 -3 -5 -4 -4 -6 -4 -2 -2 -9 -6 -3 -3 -3 -4 -13
+* -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 1
diff --git a/src/jaligner/matrix/matrices/PAM500 b/src/jaligner/matrix/matrices/PAM500
new file mode 100644
index 0000000..c477af8
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM500
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 500 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.401, Entropy = 0.0803 bits
+#
+# Lowest score = -9, Highest score = 34
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
+R -1 5 1 0 -4 2 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
+N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
+D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
+C -2 -4 -3 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
+Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
+E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -1 -5 0 1 0 -7 -5 -1 2 2 0 -9
+G 1 -1 1 1 -3 0 1 4 -1 -2 -3 0 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
+H 0 2 1 1 -4 2 1 -1 4 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
+I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
+L -1 -2 -2 -3 -6 -2 -3 -3 -2 4 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
+K 0 4 1 1 -5 1 1 0 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
+M -1 0 -1 -2 -5 -1 -1 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -1 -1 0 -9
+F -3 -4 -4 -5 -3 -4 -5 -5 -2 2 4 -5 1 13 -4 -3 -3 3 13 0 -4 -5 -2 -9
+P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 1 0 -9
+S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
+T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
+W -6 4 -5 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
+Y -3 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -1 -4 -4 -2 -9
+V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -1 3 -1 -1 0 -9
+B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -1 -4 0 1 0 -6 -4 -1 2 2 0 -9
+Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
+X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/src/jaligner/matrix/matrices/PAM60 b/src/jaligner/matrix/matrices/PAM60
new file mode 100644
index 0000000..269b2f5
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM60
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 60 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -3.21, Entropy = 1.79 bits
+#
+# Lowest score = -12, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -5 -2 -2 -5 -3 -1 0 -5 -3 -4 -5 -3 -6 0 1 1 -10 -6 -1 -2 -2 -2 -12
+R -5 8 -3 -6 -6 0 -6 -7 0 -4 -6 2 -2 -7 -2 -2 -4 0 -8 -5 -5 -2 -4 -12
+N -2 -3 6 2 -7 -2 0 -1 1 -4 -5 0 -6 -6 -4 1 -1 -6 -3 -5 5 -1 -2 -12
+D -2 -6 2 7 -10 -1 3 -2 -2 -5 -9 -2 -7 -11 -5 -2 -3 -11 -8 -6 5 2 -3 -12
+C -5 -6 -7 -10 9 -10 -10 -7 -6 -4 -11 -10 -10 -9 -6 -1 -5 -12 -2 -4 -9 -10 -6 -12
+Q -3 0 -2 -1 -10 7 2 -5 2 -5 -3 -1 -2 -9 -1 -3 -4 -9 -8 -5 -1 6 -3 -12
+E -1 -6 0 3 -10 2 7 -2 -3 -4 -7 -3 -5 -10 -3 -2 -4 -12 -7 -4 2 5 -3 -12
+G 0 -7 -1 -2 -7 -5 -2 6 -6 -7 -8 -5 -6 -7 -4 0 -3 -11 -10 -4 -2 -3 -3 -12
+H -5 0 1 -2 -6 2 -3 -6 8 -6 -4 -4 -7 -4 -2 -4 -5 -5 -2 -5 0 0 -3 -12
+I -3 -4 -4 -5 -4 -5 -4 -7 -6 7 0 -4 1 -1 -6 -4 -1 -10 -4 3 -4 -4 -3 -12
+L -4 -6 -5 -9 -11 -3 -7 -8 -4 0 6 -6 2 -1 -5 -6 -5 -4 -5 -1 -7 -5 -4 -12
+K -5 2 0 -2 -10 -1 -3 -5 -4 -4 -6 6 0 -10 -4 -2 -2 -8 -7 -6 -1 -2 -3 -12
+M -3 -2 -6 -7 -10 -2 -5 -6 -7 1 2 0 10 -2 -6 -4 -2 -9 -7 0 -6 -4 -3 -12
+F -6 -7 -6 -11 -9 -9 -10 -7 -4 -1 -1 -10 -2 8 -7 -5 -6 -3 3 -5 -8 -10 -5 -12
+P 0 -2 -4 -5 -6 -1 -3 -4 -2 -6 -5 -4 -6 -7 7 0 -2 -10 -10 -4 -4 -2 -3 -12
+S 1 -2 1 -2 -1 -3 -2 0 -4 -4 -6 -2 -4 -5 0 5 1 -4 -5 -4 0 -3 -2 -12
+T 1 -4 -1 -3 -5 -4 -4 -3 -5 -1 -5 -2 -2 -6 -2 1 6 -9 -5 -1 -2 -4 -2 -12
+W -10 0 -6 -11 -12 -9 -12 -11 -5 -10 -4 -8 -9 -3 -10 -4 -9 13 -3 -11 -8 -11 -8 -12
+Y -6 -8 -3 -8 -2 -8 -7 -10 -2 -4 -5 -7 -7 3 -10 -5 -5 -3 9 -5 -5 -7 -5 -12
+V -1 -5 -5 -6 -4 -5 -4 -4 -5 3 -1 -6 0 -5 -4 -4 -1 -11 -5 6 -5 -5 -3 -12
+B -2 -5 5 5 -9 -1 2 -2 0 -4 -7 -1 -6 -8 -4 0 -2 -8 -5 -5 5 1 -3 -12
+Z -2 -2 -1 2 -10 6 5 -3 0 -4 -5 -2 -4 -10 -2 -3 -4 -11 -7 -5 1 5 -3 -12
+X -2 -4 -2 -3 -6 -3 -3 -3 -3 -3 -4 -3 -3 -5 -3 -2 -2 -8 -5 -3 -3 -3 -3 -12
+* -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 1
diff --git a/src/jaligner/matrix/matrices/PAM70 b/src/jaligner/matrix/matrices/PAM70
new file mode 100644
index 0000000..f445237
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM70
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.77, Entropy = 1.60 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -1 -2 -11
+R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -2 -3 -11
+N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -1 -2 -11
+D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 2 -3 -11
+C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -9 -6 -11
+Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 5 -2 -11
+E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -3 -11
+G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -3 -3 -11
+H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 1 -3 -11
+I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 -4 -3 -11
+L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 -4 -4 -11
+K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -2 -3 -11
+M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 -3 -3 -11
+F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -9 -5 -11
+P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -2 -3 -11
+S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -2 -1 -11
+T 1 -4 0 -2 -5 -3 -3 -3 -4 -1 -4 -1 -2 -6 -2 2 6 -8 -4 -1 -1 -3 -2 -11
+W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -10 -7 -11
+Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -7 -5 -11
+V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 -4 -2 -11
+B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 1 -2 -11
+Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 5 -3 -11
+X -2 -3 -2 -3 -6 -2 -3 -3 -3 -3 -4 -3 -3 -5 -3 -1 -2 -7 -5 -2 -2 -3 -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
diff --git a/src/jaligner/matrix/matrices/PAM80 b/src/jaligner/matrix/matrices/PAM80
new file mode 100644
index 0000000..d694051
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM80
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.55, Entropy = 1.44 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -4 -1 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -5 0 1 1 -8 -5 0 -1 -1 -1 -11
+R -4 7 -2 -5 -5 0 -4 -6 0 -3 -5 2 -2 -6 -2 -1 -3 0 -7 -5 -3 -1 -3 -11
+N -1 -2 5 3 -6 -1 0 -1 2 -3 -5 0 -4 -5 -3 1 0 -5 -3 -4 4 0 -1 -11
+D -1 -5 3 6 -9 0 4 -1 -1 -4 -7 -2 -6 -9 -4 -1 -2 -10 -7 -5 5 2 -3 -11
+C -4 -5 -6 -9 9 -9 -9 -6 -5 -4 -9 -9 -8 -8 -5 -1 -4 -10 -2 -3 -7 -9 -5 -11
+Q -2 0 -1 0 -9 7 2 -4 2 -4 -3 -1 -2 -8 -1 -3 -3 -8 -7 -4 0 5 -2 -11
+E -1 -4 0 4 -9 2 6 -2 -2 -3 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -2 -11
+G 0 -6 -1 -1 -6 -4 -2 6 -5 -6 -7 -4 -5 -6 -3 0 -2 -10 -8 -3 -1 -2 -3 -11
+H -4 0 2 -1 -5 2 -2 -5 8 -5 -4 -3 -5 -3 -2 -3 -4 -4 -1 -4 0 1 -2 -11
+I -2 -3 -3 -4 -4 -4 -3 -6 -5 7 1 -4 1 0 -5 -4 -1 -8 -3 3 -4 -4 -2 -11
+L -4 -5 -5 -7 -9 -3 -6 -7 -4 1 6 -5 2 0 -4 -5 -4 -3 -4 0 -6 -4 -3 -11
+K -4 2 0 -2 -9 -1 -2 -4 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -6 -5 -1 -1 -3 -11
+M -3 -2 -4 -6 -8 -2 -4 -5 -5 1 2 0 9 -2 -5 -3 -2 -7 -6 1 -5 -3 -2 -11
+F -5 -6 -5 -9 -8 -8 -9 -6 -3 0 0 -9 -2 8 -7 -4 -5 -2 4 -4 -7 -8 -5 -11
+P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -4 -4 -5 -7 7 0 -2 -9 -8 -3 -3 -2 -2 -11
+S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -5 -2 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -11
+T 1 -3 0 -2 -4 -3 -3 -2 -4 -1 -4 -1 -2 -5 -2 2 5 -8 -4 -1 -1 -3 -1 -11
+W -8 0 -5 -10 -10 -8 -11 -10 -4 -8 -3 -7 -7 -2 -9 -3 -8 13 -2 -10 -7 -9 -7 -11
+Y -5 -7 -3 -7 -2 -7 -6 -8 -1 -3 -4 -6 -6 4 -8 -4 -4 -2 9 -5 -4 -6 -4 -11
+V 0 -5 -4 -5 -3 -4 -4 -3 -4 3 0 -5 1 -4 -3 -3 -1 -10 -5 6 -4 -4 -2 -11
+B -1 -3 4 5 -7 0 2 -1 0 -4 -6 -1 -5 -7 -3 0 -1 -7 -4 -4 5 2 -2 -11
+Z -1 -1 0 2 -9 5 5 -2 1 -4 -4 -1 -3 -8 -2 -2 -3 -9 -6 -4 2 5 -2 -11
+X -1 -3 -1 -3 -5 -2 -2 -3 -2 -2 -3 -3 -2 -5 -2 -1 -1 -7 -4 -2 -2 -2 -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
diff --git a/src/jaligner/matrix/matrices/PAM90 b/src/jaligner/matrix/matrices/PAM90
new file mode 100644
index 0000000..b0cc807
--- /dev/null
+++ b/src/jaligner/matrix/matrices/PAM90
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 90 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.26, Entropy = 1.30 bits
+#
+# Lowest score = -10, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -4 -1 -1 -3 -2 0 0 -4 -2 -3 -3 -2 -5 0 1 1 -8 -5 0 -1 -1 -1 -10
+R -4 7 -2 -5 -5 0 -4 -5 1 -3 -5 2 -2 -6 -1 -1 -3 0 -6 -4 -3 -1 -2 -10
+N -1 -2 5 3 -6 -1 0 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -4 4 0 -1 -10
+D -1 -5 3 6 -8 0 4 -1 -1 -4 -7 -2 -5 -8 -4 -1 -2 -9 -6 -4 5 3 -2 -10
+C -3 -5 -6 -8 9 -8 -8 -5 -5 -3 -9 -8 -8 -7 -5 -1 -4 -10 -1 -3 -7 -8 -5 -10
+Q -2 0 -1 0 -8 6 2 -3 2 -4 -3 -1 -2 -7 -1 -2 -3 -7 -6 -4 0 5 -2 -10
+E 0 -4 0 4 -8 2 6 -1 -1 -3 -5 -2 -4 -8 -2 -2 -2 -10 -6 -3 2 5 -2 -10
+G 0 -5 -1 -1 -5 -3 -1 5 -5 -5 -6 -4 -5 -6 -3 0 -2 -9 -8 -3 -1 -2 -2 -10
+H -4 1 2 -1 -5 2 -1 -5 8 -5 -3 -2 -5 -3 -2 -3 -3 -4 -1 -4 1 1 -2 -10
+I -2 -3 -3 -4 -3 -4 -3 -5 -5 6 1 -3 1 0 -4 -3 0 -8 -3 3 -3 -3 -2 -10
+L -3 -5 -4 -7 -9 -3 -5 -6 -3 1 6 -5 2 0 -4 -5 -3 -3 -3 0 -5 -4 -3 -10
+K -3 2 1 -2 -8 -1 -2 -4 -2 -3 -5 5 0 -8 -3 -1 -1 -6 -6 -5 0 -1 -2 -10
+M -2 -2 -4 -5 -8 -2 -4 -5 -5 1 2 0 9 -1 -4 -3 -2 -7 -6 1 -5 -3 -2 -10
+F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -8 -1 8 -6 -4 -5 -2 4 -4 -6 -8 -4 -10
+P 0 -1 -2 -4 -5 -1 -2 -3 -2 -4 -4 -3 -4 -6 7 0 -1 -8 -8 -3 -3 -2 -2 -10
+S 1 -1 1 -1 -1 -2 -2 0 -3 -3 -5 -1 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -10
+T 1 -3 0 -2 -4 -3 -2 -2 -3 0 -3 -1 -2 -5 -1 2 5 -7 -4 -1 -1 -2 -1 -10
+W -8 0 -5 -9 -10 -7 -10 -9 -4 -8 -3 -6 -7 -2 -8 -3 -7 13 -2 -9 -7 -8 -6 -10
+Y -5 -6 -2 -6 -1 -6 -6 -8 -1 -3 -3 -6 -6 4 -8 -4 -4 -2 9 -4 -4 -6 -4 -10
+V 0 -4 -4 -4 -3 -4 -3 -3 -4 3 0 -5 1 -4 -3 -3 -1 -9 -4 6 -4 -3 -2 -10
+B -1 -3 4 5 -7 0 2 -1 1 -3 -5 0 -5 -6 -3 0 -1 -7 -4 -4 4 2 -2 -10
+Z -1 -1 0 3 -8 5 5 -2 1 -3 -4 -1 -3 -8 -2 -2 -2 -8 -6 -3 2 5 -2 -10
+X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/src/jaligner/matrix/package.html b/src/jaligner/matrix/package.html
new file mode 100644
index 0000000..d5583c2
--- /dev/null
+++ b/src/jaligner/matrix/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.1 2005/01/11 16:48:25 ahmed Exp $--></head>
+<body bgcolor="white">
+Scoring matrices package.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/package.html b/src/jaligner/package.html
new file mode 100644
index 0000000..614c03d
--- /dev/null
+++ b/src/jaligner/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.5 2004/11/25 19:07:02 ahmed Exp $--></head>
+<body bgcolor="white">
+Core classes for the implementation of Smith-Waterman-Gotoh algorithm
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/test/AlignmentScoreChecker.java b/src/jaligner/test/AlignmentScoreChecker.java
new file mode 100644
index 0000000..4a57cc5
--- /dev/null
+++ b/src/jaligner/test/AlignmentScoreChecker.java
@@ -0,0 +1,131 @@
+/*
+ * $Id: AlignmentScoreChecker.java,v 1.2 2005/04/18 14:06:15 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.test;
+
+import jaligner.Alignment;
+import jaligner.Sequence;
+import jaligner.SmithWatermanGotoh;
+import jaligner.formats.Format;
+import jaligner.formats.Pair;
+import jaligner.matrix.Matrix;
+import jaligner.matrix.MatrixLoader;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.Random;
+
+/**
+ * Testing the scores of the alignments of the SmithWaterman algorithm
+ *
+ * @author Bram Minnaert
+ */
+
+public class AlignmentScoreChecker {
+
+ public static void main(String[] args) {
+
+ int numberOfTests = Integer.parseInt(args[0]);
+ int sequencesSize = Integer.parseInt(args[1]);
+ Random random = new Random();
+ Format format = new Pair();
+
+ try {
+ ArrayList matrices = new ArrayList();
+ for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) {
+ matrices.add(i.next());
+ }
+ int countOfMatrices = matrices.size();
+
+ int i = 1;
+ while (i <= numberOfTests) {
+
+ System.gc();
+
+ String s1 = RandomSequenceGenerator.generate(sequencesSize);
+ String s2 = RandomSequenceGenerator.generate(sequencesSize);
+
+ int o = random.nextInt(50);
+ int e = random.nextInt(10);
+
+ if (s1.length() > 0 && s2.length() > 0 && o >= e) {
+
+ Matrix matrix = (Matrix) MatrixLoader
+ .load((String) matrices.get(random
+ .nextInt(countOfMatrices)));
+ Sequence seq1 = new Sequence(s1);
+ Sequence seq2 = new Sequence(s2);
+
+ Alignment alignment1 = SmithWatermanGotoh.align(seq1, seq2,
+ matrix, o, e);
+
+ if (!alignment1.checkScore()) {
+ System.err.println("Invalid alignment found:");
+ System.err.println("Sequence 1 = " + s1);
+ System.err.println("Sequence 2 = " + s2);
+ System.err.println(format.format(alignment1));
+ System.err.println(alignment1.getSummary());
+ System.err
+ .println("The score of the alignment above is: "
+ + alignment1.calculateScore());
+ System.exit(1);
+ }
+
+ Alignment alignment2 = SmithWatermanGotoh.align(seq2, seq1,
+ matrix, o, e);
+ if (!alignment1.checkScore()) {
+ System.err.println("Invalid alignment found:");
+ System.err.println("Sequence 1 = " + s2);
+ System.err.println("Sequence 2 = " + s1);
+ System.err.println(format.format(alignment2));
+ System.err.println(alignment2.getSummary());
+ System.err
+ .println("The score of the alignment above is: "
+ + alignment2.calculateScore());
+ System.exit(1);
+ }
+
+ if (alignment1.getScore() != alignment2.getScore()) {
+ System.err.println("Not symmetric alignment:");
+
+ System.err.println("Alignment #1: ");
+ System.err.println("Sequence 1 = " + s1);
+ System.err.println("Sequence 2 = " + s2);
+ System.err.println(format.format(alignment1));
+ System.err.println(alignment1.getSummary());
+
+ System.err.println();
+
+ System.err.println("Alignment #2: ");
+ System.err.println("Sequence 1 = " + s2);
+ System.err.println("Sequence 2 = " + s1);
+ System.err.println(format.format(alignment2));
+ System.err.println(alignment2.getSummary());
+
+ System.exit(1);
+ }
+ }
+ System.out.println("Processed " + i + "/" + numberOfTests);
+ i++;
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ System.exit(1);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/test/RandomSequenceGenerator.java b/src/jaligner/test/RandomSequenceGenerator.java
new file mode 100644
index 0000000..f77c0dd
--- /dev/null
+++ b/src/jaligner/test/RandomSequenceGenerator.java
@@ -0,0 +1,75 @@
+/*
+ * $Id: RandomSequenceGenerator.java,v 1.1 2005/04/03 19:38:21 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.test;
+
+import java.util.Random;
+
+/**
+ * This class contains a random generator for protein sequences.
+ *
+ * @author Bram Minnaert
+ */
+
+public class RandomSequenceGenerator {
+
+ /**
+ * All possible characters
+ */
+ private static final char[] CHARS = {
+ 'A', 'R', 'N', 'D', 'C', 'Q', 'E',
+ 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P',
+ 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X'};
+
+ /**
+ * Number of possible characters
+ */
+ private static final int NUMBER_OF_CHARS = CHARS.length;
+
+ /**
+ * Random generator
+ */
+ private static Random random = new Random();
+
+ /**
+ * Returns random sequence
+ * @param length Size of the sequence
+ * @return Random sequence
+ */
+ public static String generate(int length) {
+ StringBuffer buffer = new StringBuffer();
+ char randomChar;
+ int randomInt;
+ for (int i = 0; i < length ; i++) {
+ randomInt = random.nextInt(NUMBER_OF_CHARS);
+ randomChar = CHARS[randomInt];
+ buffer.append(randomChar);
+ }
+ return buffer.toString();
+ }
+
+ /**
+ * Displays 10 random protein sequences with length 50.
+ * @param args no args
+ */
+ public static void main(String[] args) {
+ for (int i = 0; i < 10; i++) {
+ System.out.println("S" + i + " = " + generate(50));
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/test/package.html b/src/jaligner/test/package.html
new file mode 100644
index 0000000..56c88e4
--- /dev/null
+++ b/src/jaligner/test/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.1 2005/04/05 02:18:51 ahmed Exp $--></head>
+<body bgcolor="white">
+Testing package.
+ at author Bram Minnaert
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/AlignCommandLine.java b/src/jaligner/ui/AlignCommandLine.java
new file mode 100644
index 0000000..bdc0df8
--- /dev/null
+++ b/src/jaligner/ui/AlignCommandLine.java
@@ -0,0 +1,93 @@
+/*
+ * $Id: AlignCommandLine.java,v 1.7 2005/04/18 05:37:52 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui;
+
+import jaligner.Alignment;
+import jaligner.Sequence;
+import jaligner.SmithWatermanGotoh;
+import jaligner.formats.Pair;
+import jaligner.matrix.Matrix;
+import jaligner.matrix.MatrixLoader;
+import jaligner.util.Commons;
+import jaligner.util.SequenceParser;
+
+import java.io.File;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Command line interface for JAligner.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+public class AlignCommandLine {
+
+ private static final Logger logger = Logger.getLogger(AlignCommandLine.class.getName());
+
+ /**
+ * @param args The command line arguments
+ */
+ public static void main(String[] args) {
+ logger.info( Commons.getJAlignerInfo() );
+
+ if (args.length == 0) {
+ new AlignWindow().setVisible(true);
+ } else {
+ if (args.length == 5) {
+ try {
+
+ String f1 = args[0]; // file name of sequence #1
+ String f2 = args[1]; // file name of sequence #1
+ String m = args[2]; // scoring matrix id or file name user-defined scoring matrix
+ float o = Float.parseFloat(args[3]); // open gap penalty
+ float e = Float.parseFloat(args[4]); // extend gap penalty
+
+ Sequence s1 = SequenceParser.parse(new File(f1));
+ Sequence s2 = SequenceParser.parse(new File(f2));
+ Matrix matrix = MatrixLoader.load(m);
+ Alignment alignment = SmithWatermanGotoh.align (s1, s2, matrix, o, e);
+ System.out.println (alignment.getSummary());
+ System.out.println (new Pair().format(alignment));
+ } catch (Exception e) {
+ logger.log(Level.SEVERE, "Failed processing the command line: " + e.getMessage(), e);
+ System.exit(1);
+ }
+ } else {
+ logger.severe( "Invalid number of arguments: " + args.length );
+ printUsage();
+ System.exit(1);
+ }
+ }
+
+ }
+
+ /**
+ * Prints the syntax for using JAligner
+ */
+ private static void printUsage( ) {
+ StringBuffer buffer = new StringBuffer();
+ buffer.append ( "\n" );
+ buffer.append ( "Usage:\n" );
+ buffer.append ( "------\n" );
+ buffer.append ( "[1] java -jar jaligner.jar <s1> <s2> <matrix> <open> <extend>\n" );
+ buffer.append ( "[2] java -jar jaligner.jar\n" );
+ buffer.append ( "\n" ) ;
+ logger.info(buffer.toString());
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/AlignWindow.form b/src/jaligner/ui/AlignWindow.form
new file mode 100644
index 0000000..20c67ee
--- /dev/null
+++ b/src/jaligner/ui/AlignWindow.form
@@ -0,0 +1,896 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.0" type="org.netbeans.modules.form.forminfo.JFrameFormInfo">
+ <NonVisualComponents>
+ <Menu class="javax.swing.JPopupMenu" name="jPopup">
+ <SubComponents>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupOpen">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+O"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.OPEN" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="79"/>
+ <Property name="text" type="java.lang.String" value="Open..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupOpenActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupSave">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+S"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.SAVE" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="83"/>
+ <Property name="text" type="java.lang.String" value="Save..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupSaveActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JSeparator" name="jPopupSeparator1">
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupCut">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+X"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.CUT" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="116"/>
+ <Property name="text" type="java.lang.String" value="Cut"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupCutActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupCopy">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+C"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.COPY" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="67"/>
+ <Property name="text" type="java.lang.String" value="Copy"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupCopyActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupPaste">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+V"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.PASTE" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="80"/>
+ <Property name="text" type="java.lang.String" value="Paste"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupPasteActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupDelete">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="DELETE"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.DELETE" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="68"/>
+ <Property name="text" type="java.lang.String" value="Delete"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupDeleteActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JSeparator" name="jPopupSeparator2">
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupPrint">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+P"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.PRINT" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="68"/>
+ <Property name="text" type="java.lang.String" value="Print"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupPrintActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JSeparator" name="jPopupSeparator3">
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jPopupSelectAll">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+A"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="65"/>
+ <Property name="text" type="java.lang.String" value="Select All"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jPopupSelectAllActionPerformed"/>
+ </Events>
+ </MenuItem>
+ </SubComponents>
+ </Menu>
+ <Component class="javax.swing.ButtonGroup" name="buttonGroupSequences">
+ </Component>
+ <Menu class="javax.swing.JMenuBar" name="jMenuBar">
+ <SubComponents>
+ <Menu class="javax.swing.JMenu" name="jMenuFile">
+ <Properties>
+ <Property name="mnemonic" type="int" value="70"/>
+ <Property name="text" type="java.lang.String" value="File"/>
+ </Properties>
+ <SubComponents>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemFileOpen">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+O"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.OPEN" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="79"/>
+ <Property name="text" type="java.lang.String" value="Open..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemFileOpenActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemFileLoadSequence1">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+1"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.OPEN" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="49"/>
+ <Property name="text" type="java.lang.String" value="Load sequence #1..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemFileLoadSequence1ActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemFileLoadSequence2">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+2"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.OPEN" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="50"/>
+ <Property name="text" type="java.lang.String" value="Load sequence #2..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemFileLoadSequence2ActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemFileLoadMatrix">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+M"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.OPEN" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="77"/>
+ <Property name="text" type="java.lang.String" value="Load scoring matrix..."/>
+ <Property name="toolTipText" type="java.lang.String" value="Load user-defined scoring matrix from file system"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemFileLoadMatrixActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JSeparator" name="jSeparatorFile">
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemFileExit">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Alt+X"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.CLOSE" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="88"/>
+ <Property name="text" type="java.lang.String" value="Exit"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemFileExitActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemFilePrint">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+P"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.PRINT" type="code"/>
+ </Property>
+ <Property name="text" type="java.lang.String" value="Print..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemFilePrintActionPerformed"/>
+ </Events>
+ </MenuItem>
+ </SubComponents>
+ </Menu>
+ <Menu class="javax.swing.JMenu" name="jMenuEdit">
+ <Properties>
+ <Property name="mnemonic" type="int" value="69"/>
+ <Property name="text" type="java.lang.String" value="Edit"/>
+ </Properties>
+ <SubComponents>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemEditCut">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+X"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.CUT" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="116"/>
+ <Property name="text" type="java.lang.String" value="Cut"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemEditCutActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemEditCopy">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+C"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.COPY" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="67"/>
+ <Property name="text" type="java.lang.String" value="Copy"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemEditCopyActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemEditPaste">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+V"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.PASTE" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="80"/>
+ <Property name="text" type="java.lang.String" value="Paste"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemEditPasteActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemEditDelete">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="DELETE"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.DELETE" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="68"/>
+ <Property name="text" type="java.lang.String" value="Delete"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemEditDeleteActionPerformed"/>
+ </Events>
+ </MenuItem>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemEditSelectAll">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="Ctrl+A"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="65"/>
+ <Property name="text" type="java.lang.String" value="Select All"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemEditSelectAllActionPerformed"/>
+ </Events>
+ </MenuItem>
+ </SubComponents>
+ </Menu>
+ <Menu class="javax.swing.JMenu" name="jMenuTools">
+ <Properties>
+ <Property name="mnemonic" type="int" value="84"/>
+ <Property name="text" type="java.lang.String" value="Tools"/>
+ </Properties>
+ <SubComponents>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemToolsRunExample">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="F5"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="69"/>
+ <Property name="text" type="java.lang.String" value="Example"/>
+ <Property name="toolTipText" type="java.lang.String" value="Aligns P53 human and P53 mouse"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemToolsRunExampleActionPerformed"/>
+ </Events>
+ </MenuItem>
+ </SubComponents>
+ </Menu>
+ <Menu class="javax.swing.JMenu" name="jMenuHelp">
+ <Properties>
+ <Property name="mnemonic" type="int" value="72"/>
+ <Property name="text" type="java.lang.String" value="Help"/>
+ </Properties>
+ <SubComponents>
+ <MenuItem class="javax.swing.JMenuItem" name="jMenuItemAbout">
+ <Properties>
+ <Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
+ <KeyStroke key="F1"/>
+ </Property>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.ABOUT" type="code"/>
+ </Property>
+ <Property name="mnemonic" type="int" value="65"/>
+ <Property name="text" type="java.lang.String" value="About..."/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jMenuItemAboutActionPerformed"/>
+ </Events>
+ </MenuItem>
+ </SubComponents>
+ </Menu>
+ </SubComponents>
+ </Menu>
+ </NonVisualComponents>
+ <Properties>
+ <Property name="defaultCloseOperation" type="int" value="0"/>
+ <Property name="title" type="java.lang.String" value="JAligner - biological pairwise sequence alignment <http://jaligner.sf.net>"/>
+ <Property name="name" type="java.lang.String" value="AlignWindow"/>
+ </Properties>
+ <SyntheticProperties>
+ <SyntheticProperty name="menuBar" type="java.lang.String" value="jMenuBar"/>
+ <SyntheticProperty name="formSizePolicy" type="int" value="1"/>
+ </SyntheticProperties>
+ <Events>
+ <EventHandler event="windowClosing" listener="java.awt.event.WindowListener" parameters="java.awt.event.WindowEvent" handler="exitForm"/>
+ </Events>
+ <AuxValues>
+ <AuxValue name="designerSize" type="java.awt.Dimension" value="-84,-19,0,5,115,114,0,18,106,97,118,97,46,97,119,116,46,68,105,109,101,110,115,105,111,110,65,-114,-39,-41,-84,95,68,20,2,0,2,73,0,6,104,101,105,103,104,116,73,0,5,119,105,100,116,104,120,112,0,0,1,-39,0,0,2,100"/>
+ </AuxValues>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JToolBar" name="jToolBar">
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="North"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBoxLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="jButtonOpen">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.OPEN" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Open..."/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonOpenActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonSave">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.SAVE" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Save..."/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonSaveActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonCut">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.CUT" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Cut"/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonCutActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonCopy">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.COPY" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Copy"/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonCopyActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonPaste">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.PASTE" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Paste"/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonPasteActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonDelete">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.DELETE" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Delete"/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonDeleteActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonPrint">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.PRINT" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Print"/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonPrintActionPerformed"/>
+ </Events>
+ </Component>
+ <Component class="javax.swing.JButton" name="jButtonExit">
+ <Properties>
+ <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code="ToolbarIcons.CLOSE" type="code"/>
+ </Property>
+ <Property name="toolTipText" type="java.lang.String" value="Exit"/>
+ <Property name="focusable" type="boolean" value="false"/>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[24, 24]"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonExitActionPerformed"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JSplitPane" name="jSplitPaneBody">
+ <Properties>
+ <Property name="orientation" type="int" value="0"/>
+ <Property name="oneTouchExpandable" type="boolean" value="true"/>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="Center"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JSplitPane" name="jSplitPaneIO">
+ <Properties>
+ <Property name="oneTouchExpandable" type="boolean" value="true"/>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout$JSplitPaneConstraintsDescription">
+ <JSplitPaneConstraints position="top"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JSplitPane" name="jSplitPaneSequences">
+ <Properties>
+ <Property name="orientation" type="int" value="0"/>
+ <Property name="oneTouchExpandable" type="boolean" value="true"/>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout$JSplitPaneConstraintsDescription">
+ <JSplitPaneConstraints position="left"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="jPanelSequence1">
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout$JSplitPaneConstraintsDescription">
+ <JSplitPaneConstraints position="top"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="jScrollPaneSequence1">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[400, 50]"/>
+ </Property>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="Center"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JTextArea" name="jTextAreaSequence1">
+ <Properties>
+ <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+ <Font name="DialogInput" size="12" style="0"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextAreaSequence1FocusGained"/>
+ <EventHandler event="mouseClicked" listener="java.awt.event.MouseListener" parameters="java.awt.event.MouseEvent" handler="jTextAreaSequence1MouseClicked"/>
+ <EventHandler event="caretUpdate" listener="javax.swing.event.CaretListener" parameters="javax.swing.event.CaretEvent" handler="jTextAreaSequence1CaretUpdate"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Component class="javax.swing.JRadioButton" name="jRadioButtonSequence1">
+ <Properties>
+ <Property name="mnemonic" type="int" value="49"/>
+ <Property name="text" type="java.lang.String" value="Sequence #1"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jRadioButtonSequence1ActionPerformed"/>
+ </Events>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="North"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelSequence2">
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout$JSplitPaneConstraintsDescription">
+ <JSplitPaneConstraints position="bottom"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Container class="javax.swing.JScrollPane" name="jScrollPaneSequence2">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[400, 50]"/>
+ </Property>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="Center"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JTextArea" name="jTextAreaSequence2">
+ <Properties>
+ <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+ <Font name="DialogInput" size="12" style="0"/>
+ </Property>
+ </Properties>
+ <Events>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextAreaSequence2FocusGained"/>
+ <EventHandler event="mouseClicked" listener="java.awt.event.MouseListener" parameters="java.awt.event.MouseEvent" handler="jTextAreaSequence2MouseClicked"/>
+ <EventHandler event="caretUpdate" listener="javax.swing.event.CaretListener" parameters="javax.swing.event.CaretEvent" handler="jTextAreaSequence2CaretUpdate"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Component class="javax.swing.JRadioButton" name="jRadioButtonSequence2">
+ <Properties>
+ <Property name="mnemonic" type="int" value="50"/>
+ <Property name="text" type="java.lang.String" value="Sequence #2"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jRadioButtonSequence2ActionPerformed"/>
+ </Events>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="North"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelAlignment">
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout$JSplitPaneConstraintsDescription">
+ <JSplitPaneConstraints position="right"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JRadioButton" name="jRadioButtonAlignment">
+ <Properties>
+ <Property name="mnemonic" type="int" value="65"/>
+ <Property name="text" type="java.lang.String" value="Alignment"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jRadioButtonAlignmentActionPerformed"/>
+ </Events>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="North"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Container class="javax.swing.JScrollPane" name="jScrollPaneAlignment">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[400, 50]"/>
+ </Property>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="Center"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JTextArea" name="jTextAreaAlignment">
+ <Properties>
+ <Property name="editable" type="boolean" value="false"/>
+ <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+ <Font name="DialogInput" size="12" style="0"/>
+ </Property>
+ <Property name="tabSize" type="int" value="0"/>
+ </Properties>
+ <Events>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextAreaAlignmentFocusGained"/>
+ <EventHandler event="mouseClicked" listener="java.awt.event.MouseListener" parameters="java.awt.event.MouseEvent" handler="jTextAreaAlignmentMouseClicked"/>
+ <EventHandler event="caretUpdate" listener="javax.swing.event.CaretListener" parameters="javax.swing.event.CaretEvent" handler="jTextAreaAlignmentCaretUpdate"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelConsole">
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JSplitPaneSupportLayout$JSplitPaneConstraintsDescription">
+ <JSplitPaneConstraints position="bottom"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JRadioButton" name="jRadioButtonConsole">
+ <Properties>
+ <Property name="mnemonic" type="int" value="67"/>
+ <Property name="text" type="java.lang.String" value="Console"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jRadioButtonConsoleActionPerformed"/>
+ </Events>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="North"/>
+ </Constraint>
+ </Constraints>
+ </Component>
+ <Container class="javax.swing.JScrollPane" name="jScrollPaneConsole">
+ <Properties>
+ <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[400, 50]"/>
+ </Property>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="Center"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JTextPane" name="jTextPaneConsole">
+ <Properties>
+ <Property name="editable" type="boolean" value="false"/>
+ </Properties>
+ <Events>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextPaneConsoleFocusGained"/>
+ <EventHandler event="mouseClicked" listener="java.awt.event.MouseListener" parameters="java.awt.event.MouseEvent" handler="jTextPaneConsoleMouseClicked"/>
+ <EventHandler event="caretUpdate" listener="javax.swing.event.CaretListener" parameters="javax.swing.event.CaretEvent" handler="jTextPaneConsoleCaretUpdate"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelControls">
+ <Properties>
+ <Property name="autoscrolls" type="boolean" value="true"/>
+ </Properties>
+ <Constraints>
+ <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout" value="org.netbeans.modules.form.compat2.layouts.DesignBorderLayout$BorderConstraintsDescription">
+ <BorderConstraints direction="South"/>
+ </Constraint>
+ </Constraints>
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignGridLayout">
+ <Property name="columns" type="int" value="0"/>
+ <Property name="rows" type="int" value="1"/>
+ </Layout>
+ <SubComponents>
+ <Container class="javax.swing.JPanel" name="jPanelScoringMatrix">
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JLabel" name="jLabelScoringMatrix">
+ <Properties>
+ <Property name="displayedMnemonic" type="int" value="77"/>
+ <Property name="horizontalAlignment" type="int" value="0"/>
+ <Property name="labelFor" type="java.awt.Component" editor="org.netbeans.modules.form.ComponentChooserEditor">
+ <ComponentRef name="jComboBoxScoringMatrix"/>
+ </Property>
+ <Property name="text" type="java.lang.String" value="Matrix"/>
+ </Properties>
+ </Component>
+ <Component class="javax.swing.JComboBox" name="jComboBoxScoringMatrix">
+ <Properties>
+ <Property name="toolTipText" type="java.lang.String" value="Scoring matrix"/>
+ <Property name="prototypeDisplayValue" type="java.lang.Object" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+ <Connection code=""BLOSUMXXX"" type="code"/>
+ </Property>
+ </Properties>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelGapOpen">
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JLabel" name="jLabelOpenGapPenalty">
+ <Properties>
+ <Property name="displayedMnemonic" type="int" value="79"/>
+ <Property name="horizontalAlignment" type="int" value="0"/>
+ <Property name="labelFor" type="java.awt.Component" editor="org.netbeans.modules.form.ComponentChooserEditor">
+ <ComponentRef name="jFormattedTextFieldGapOpen"/>
+ </Property>
+ <Property name="text" type="java.lang.String" value="Open"/>
+ </Properties>
+ </Component>
+ <Component class="javax.swing.JFormattedTextField" name="jFormattedTextFieldGapOpen">
+ <Properties>
+ <Property name="columns" type="int" value="3"/>
+ <Property name="toolTipText" type="java.lang.String" value="Gap open penalty"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new JFormattedTextField(new DecimalFormat("##0.0##"));"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelGapExtend">
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JLabel" name="jLabelExtendGapPenalty">
+ <Properties>
+ <Property name="displayedMnemonic" type="int" value="69"/>
+ <Property name="horizontalAlignment" type="int" value="0"/>
+ <Property name="labelFor" type="java.awt.Component" editor="org.netbeans.modules.form.ComponentChooserEditor">
+ <ComponentRef name="jFormattedTextFieldGapExtend"/>
+ </Property>
+ <Property name="text" type="java.lang.String" value="Extend"/>
+ </Properties>
+ </Component>
+ <Component class="javax.swing.JFormattedTextField" name="jFormattedTextFieldGapExtend">
+ <Properties>
+ <Property name="columns" type="int" value="3"/>
+ <Property name="toolTipText" type="java.lang.String" value="Gap extend penalty"/>
+ </Properties>
+ <AuxValues>
+ <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new JFormattedTextField(new DecimalFormat("##0.0##"));"/>
+ </AuxValues>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelOutputFormat">
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JLabel" name="jLabelOutputFormat">
+ <Properties>
+ <Property name="displayedMnemonic" type="int" value="70"/>
+ <Property name="labelFor" type="java.awt.Component" editor="org.netbeans.modules.form.ComponentChooserEditor">
+ <ComponentRef name="jComboBoxOutputFormat"/>
+ </Property>
+ <Property name="text" type="java.lang.String" value="Format"/>
+ </Properties>
+ </Component>
+ <Component class="javax.swing.JComboBox" name="jComboBoxOutputFormat">
+ <Properties>
+ <Property name="toolTipText" type="java.lang.String" value="Alignment output format"/>
+ <Property name="opaque" type="boolean" value="false"/>
+ </Properties>
+ </Component>
+ </SubComponents>
+ </Container>
+ <Container class="javax.swing.JPanel" name="jPanelGo">
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignFlowLayout"/>
+ <SubComponents>
+ <Component class="javax.swing.JButton" name="jButtonGo">
+ <Properties>
+ <Property name="mnemonic" type="int" value="71"/>
+ <Property name="text" type="java.lang.String" value="Go"/>
+ </Properties>
+ <Events>
+ <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButtonGoActionPerformed"/>
+ </Events>
+ </Component>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+ </Container>
+ </SubComponents>
+</Form>
diff --git a/src/jaligner/ui/AlignWindow.java b/src/jaligner/ui/AlignWindow.java
new file mode 100644
index 0000000..8cd7f6e
--- /dev/null
+++ b/src/jaligner/ui/AlignWindow.java
@@ -0,0 +1,1679 @@
+/*
+ * $Id: AlignWindow.java,v 1.95 2005/05/03 16:42:21 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui;
+
+import jaligner.Alignment;
+import jaligner.Sequence;
+import jaligner.SmithWatermanGotoh;
+import jaligner.example.Example;
+import jaligner.formats.CLUSTAL;
+import jaligner.formats.FASTA;
+import jaligner.formats.FormatFactory;
+import jaligner.formats.Pair;
+import jaligner.matrix.Matrix;
+import jaligner.matrix.MatrixLoader;
+import jaligner.ui.clipboard.ClipboardListener;
+import jaligner.ui.clipboard.ClipboardPoller;
+import jaligner.ui.filechooser.FileChooserFactory;
+import jaligner.ui.filechooser.NamedInputStream;
+import jaligner.ui.images.ToolbarIcons;
+import jaligner.ui.logging.DocumentHandler;
+import jaligner.ui.util.TextComponentUtil;
+import jaligner.ui.util.TextComponentUtilException;
+import jaligner.util.Commons;
+import jaligner.util.SequenceParser;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Image;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.net.URL;
+import java.text.DecimalFormat;
+import java.util.Collection;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.AbstractAction;
+import javax.swing.AbstractButton;
+import javax.swing.Action;
+import javax.swing.JComboBox;
+import javax.swing.JFormattedTextField;
+import javax.swing.JOptionPane;
+import javax.swing.JTextArea;
+import javax.swing.KeyStroke;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.text.JTextComponent;
+
+/**
+ * Graphical user inteface for JAligner.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class AlignWindow extends javax.swing.JFrame implements ClipboardListener, DocumentListener {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3257844376876364850L;
+
+ /**
+ * Window width
+ */
+ private static final int WINDOW_WIDTH = 800;
+
+ /**
+ * Window height
+ */
+ private static final int WINDOW_HEIGHT = 600;
+
+ /**
+ * Default open gap penalty
+ */
+ private static final float DEFAULT_OPEN_GAP_PENALTY = 10f;
+
+ /**
+ * Default extend gap penalty
+ */
+ private static final float DEFAULT_EXTEND_GAP_PENALTY = 0.5f;
+
+ /**
+ * Default scoring matrix
+ */
+ private static final String DEFAULT_SCORING_MATRIX = "BLOSUM62";
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger.getLogger(AlignWindow.class.getName());
+
+ /**
+ * Clipboard poller thread
+ */
+ private ClipboardPoller clipboardPoller = null;
+
+ /**
+ * Loaded scoring matrices
+ */
+ private HashMap matrices = new HashMap();
+
+ /**
+ * Current text component
+ */
+ private JTextComponent currentTextComponent = null;
+
+ // The actions
+ public Action nextFocusAction = new AbstractAction("Move Focus Forwards") {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3763091972940183858L;
+
+ public void actionPerformed(ActionEvent evt) {
+ ((Component)evt.getSource()).transferFocus();
+ }
+ };
+
+ public Action prevFocusAction = new AbstractAction("Move Focus Backwards") {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3257844402628997943L;
+
+ public void actionPerformed(ActionEvent evt) {
+ ((Component)evt.getSource()).transferFocusBackward();
+ }
+ };
+
+ /**
+ * Constructor
+ */
+ public AlignWindow() {
+ initComponents();
+
+ logger.addHandler(new DocumentHandler(jTextPaneConsole));
+
+ try {
+ // Set the icon for the frame
+ URL url = getClass().getResource( ToolbarIcons.GIFS_HOME + "jaligner.gif");
+ if (url != null) {
+ Image image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+ setIconImage(image);
+ } else {
+ logger.warning("Image URL is NULL");
+ }
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed setting the frame image: " + e.getMessage(), e);
+ }
+
+ jMenuItemFileOpen.setVisible(false);
+
+ jFormattedTextFieldGapOpen.setValue(new Float(DEFAULT_OPEN_GAP_PENALTY));
+ jFormattedTextFieldGapExtend.setValue(new Float(DEFAULT_EXTEND_GAP_PENALTY));
+
+ Collection matrices = null;
+ try {
+ matrices = MatrixLoader.list(false);
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting list of scoring matrices: " + e.getMessage(), e);
+ }
+ if (matrices != null) {
+ populateComboBox(jComboBoxScoringMatrix, matrices, DEFAULT_SCORING_MATRIX);
+ }
+
+ FormatFactory.getInstance().registerFormat(new CLUSTAL());
+ FormatFactory.getInstance().registerFormat(new Pair());
+ FormatFactory.getInstance().registerFormat(new FASTA());
+
+ Collection formats = FormatFactory.getInstance().getFormats();
+ String[] outputFormats = new String[formats.size()];
+ Iterator i = formats.iterator();
+ for (int j = 0; i.hasNext(); j++) {
+ outputFormats[j] = (String) i.next();
+ }
+ populateComboBox(jComboBoxOutputFormat, outputFormats, null);
+
+ jTextAreaSequence1.getDocument().addDocumentListener(this);
+ jTextAreaSequence2.getDocument().addDocumentListener(this);
+ jTextAreaAlignment.getDocument().addDocumentListener(this);
+
+ // Add actions
+ jTextAreaSequence1.getInputMap().put(KeyStroke.getKeyStroke("TAB"), nextFocusAction.getClass().getName());
+ jTextAreaSequence1.getActionMap().put(nextFocusAction.getClass().getName(), nextFocusAction);
+ jTextAreaSequence1.getInputMap().put(KeyStroke.getKeyStroke("shift TAB"), prevFocusAction.getClass().getName());
+ jTextAreaSequence1.getActionMap().put(prevFocusAction.getClass().getName(), prevFocusAction);
+
+ jTextAreaSequence2.getInputMap().put(KeyStroke.getKeyStroke("TAB"), nextFocusAction.getClass().getName());
+ jTextAreaSequence2.getActionMap().put(nextFocusAction.getClass().getName(), nextFocusAction);
+ jTextAreaSequence2.getInputMap().put(KeyStroke.getKeyStroke("shift TAB"), prevFocusAction.getClass().getName());
+ jTextAreaSequence2.getActionMap().put(prevFocusAction.getClass().getName(), prevFocusAction);
+
+ // Add radio buttons to group
+ buttonGroupSequences.add(jRadioButtonSequence1);
+ buttonGroupSequences.add(jRadioButtonSequence2);
+ buttonGroupSequences.add(jRadioButtonAlignment);
+ buttonGroupSequences.add(jRadioButtonConsole);
+
+ // Split the space
+ jSplitPaneBody.setResizeWeight(.9D);
+ jSplitPaneIO.setResizeWeight(.5D);
+ jSplitPaneSequences.setResizeWeight(.5D);
+
+ // Set the focus on the text area for sequence #1
+ jTextAreaSequence1.requestFocus();
+
+ // Start the clipboard checker
+ clipboardPoller = new ClipboardPoller(this);
+ clipboardPoller.start();
+
+ // Hide the print menu item in under the File menu
+ jMenuItemFilePrint.setVisible(false);
+
+ // Set the frame size
+ this.setSize(WINDOW_WIDTH, WINDOW_HEIGHT);
+ }
+
+ private void initComponents() {//GEN-BEGIN:initComponents
+ jPopup = new javax.swing.JPopupMenu();
+ jPopupOpen = new javax.swing.JMenuItem();
+ jPopupSave = new javax.swing.JMenuItem();
+ jPopupSeparator1 = new javax.swing.JSeparator();
+ jPopupCut = new javax.swing.JMenuItem();
+ jPopupCopy = new javax.swing.JMenuItem();
+ jPopupPaste = new javax.swing.JMenuItem();
+ jPopupDelete = new javax.swing.JMenuItem();
+ jPopupSeparator2 = new javax.swing.JSeparator();
+ jPopupPrint = new javax.swing.JMenuItem();
+ jPopupSeparator3 = new javax.swing.JSeparator();
+ jPopupSelectAll = new javax.swing.JMenuItem();
+ buttonGroupSequences = new javax.swing.ButtonGroup();
+ jToolBar = new javax.swing.JToolBar();
+ jButtonOpen = new javax.swing.JButton();
+ jButtonSave = new javax.swing.JButton();
+ jButtonCut = new javax.swing.JButton();
+ jButtonCopy = new javax.swing.JButton();
+ jButtonPaste = new javax.swing.JButton();
+ jButtonDelete = new javax.swing.JButton();
+ jButtonPrint = new javax.swing.JButton();
+ jButtonExit = new javax.swing.JButton();
+ jSplitPaneBody = new javax.swing.JSplitPane();
+ jSplitPaneIO = new javax.swing.JSplitPane();
+ jSplitPaneSequences = new javax.swing.JSplitPane();
+ jPanelSequence1 = new javax.swing.JPanel();
+ jScrollPaneSequence1 = new javax.swing.JScrollPane();
+ jTextAreaSequence1 = new javax.swing.JTextArea();
+ jRadioButtonSequence1 = new javax.swing.JRadioButton();
+ jPanelSequence2 = new javax.swing.JPanel();
+ jScrollPaneSequence2 = new javax.swing.JScrollPane();
+ jTextAreaSequence2 = new javax.swing.JTextArea();
+ jRadioButtonSequence2 = new javax.swing.JRadioButton();
+ jPanelAlignment = new javax.swing.JPanel();
+ jRadioButtonAlignment = new javax.swing.JRadioButton();
+ jScrollPaneAlignment = new javax.swing.JScrollPane();
+ jTextAreaAlignment = new javax.swing.JTextArea();
+ jPanelConsole = new javax.swing.JPanel();
+ jRadioButtonConsole = new javax.swing.JRadioButton();
+ jScrollPaneConsole = new javax.swing.JScrollPane();
+ jTextPaneConsole = new javax.swing.JTextPane();
+ jPanelControls = new javax.swing.JPanel();
+ jPanelScoringMatrix = new javax.swing.JPanel();
+ jLabelScoringMatrix = new javax.swing.JLabel();
+ jComboBoxScoringMatrix = new javax.swing.JComboBox();
+ jPanelGapOpen = new javax.swing.JPanel();
+ jLabelOpenGapPenalty = new javax.swing.JLabel();
+ jFormattedTextFieldGapOpen = new JFormattedTextField(new DecimalFormat("##0.0##"));
+ jPanelGapExtend = new javax.swing.JPanel();
+ jLabelExtendGapPenalty = new javax.swing.JLabel();
+ jFormattedTextFieldGapExtend = new JFormattedTextField(new DecimalFormat("##0.0##"));
+ jPanelOutputFormat = new javax.swing.JPanel();
+ jLabelOutputFormat = new javax.swing.JLabel();
+ jComboBoxOutputFormat = new javax.swing.JComboBox();
+ jPanelGo = new javax.swing.JPanel();
+ jButtonGo = new javax.swing.JButton();
+ jMenuBar = new javax.swing.JMenuBar();
+ jMenuFile = new javax.swing.JMenu();
+ jMenuItemFileOpen = new javax.swing.JMenuItem();
+ jMenuItemFileLoadSequence1 = new javax.swing.JMenuItem();
+ jMenuItemFileLoadSequence2 = new javax.swing.JMenuItem();
+ jMenuItemFileLoadMatrix = new javax.swing.JMenuItem();
+ jSeparatorFile = new javax.swing.JSeparator();
+ jMenuItemFileExit = new javax.swing.JMenuItem();
+ jMenuItemFilePrint = new javax.swing.JMenuItem();
+ jMenuEdit = new javax.swing.JMenu();
+ jMenuItemEditCut = new javax.swing.JMenuItem();
+ jMenuItemEditCopy = new javax.swing.JMenuItem();
+ jMenuItemEditPaste = new javax.swing.JMenuItem();
+ jMenuItemEditDelete = new javax.swing.JMenuItem();
+ jMenuItemEditSelectAll = new javax.swing.JMenuItem();
+ jMenuTools = new javax.swing.JMenu();
+ jMenuItemToolsRunExample = new javax.swing.JMenuItem();
+ jMenuHelp = new javax.swing.JMenu();
+ jMenuItemAbout = new javax.swing.JMenuItem();
+
+ jPopupOpen.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupOpen.setIcon(ToolbarIcons.OPEN);
+ jPopupOpen.setMnemonic('O');
+ jPopupOpen.setText("Open...");
+ jPopupOpen.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupOpenActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupOpen);
+
+ jPopupSave.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupSave.setIcon(ToolbarIcons.SAVE);
+ jPopupSave.setMnemonic('S');
+ jPopupSave.setText("Save...");
+ jPopupSave.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupSaveActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupSave);
+
+ jPopup.add(jPopupSeparator1);
+
+ jPopupCut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupCut.setIcon(ToolbarIcons.CUT);
+ jPopupCut.setMnemonic('t');
+ jPopupCut.setText("Cut");
+ jPopupCut.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupCutActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupCut);
+
+ jPopupCopy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupCopy.setIcon(ToolbarIcons.COPY);
+ jPopupCopy.setMnemonic('C');
+ jPopupCopy.setText("Copy");
+ jPopupCopy.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupCopyActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupCopy);
+
+ jPopupPaste.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupPaste.setIcon(ToolbarIcons.PASTE);
+ jPopupPaste.setMnemonic('P');
+ jPopupPaste.setText("Paste");
+ jPopupPaste.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupPasteActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupPaste);
+
+ jPopupDelete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0));
+ jPopupDelete.setIcon(ToolbarIcons.DELETE);
+ jPopupDelete.setMnemonic('D');
+ jPopupDelete.setText("Delete");
+ jPopupDelete.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupDeleteActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupDelete);
+
+ jPopup.add(jPopupSeparator2);
+
+ jPopupPrint.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupPrint.setIcon(ToolbarIcons.PRINT);
+ jPopupPrint.setMnemonic('D');
+ jPopupPrint.setText("Print");
+ jPopupPrint.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupPrintActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupPrint);
+
+ jPopup.add(jPopupSeparator3);
+
+ jPopupSelectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK));
+ jPopupSelectAll.setMnemonic('A');
+ jPopupSelectAll.setText("Select All");
+ jPopupSelectAll.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jPopupSelectAllActionPerformed(evt);
+ }
+ });
+
+ jPopup.add(jPopupSelectAll);
+
+ setDefaultCloseOperation(javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE);
+ setTitle("JAligner - biological pairwise sequence alignment <http://jaligner.sf.net>");
+ setName("AlignWindow");
+ addWindowListener(new java.awt.event.WindowAdapter() {
+ public void windowClosing(java.awt.event.WindowEvent evt) {
+ exitForm(evt);
+ }
+ });
+
+ jButtonOpen.setIcon(ToolbarIcons.OPEN);
+ jButtonOpen.setToolTipText("Open...");
+ jButtonOpen.setFocusable(false);
+ jButtonOpen.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonOpen.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonOpenActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonOpen);
+
+ jButtonSave.setIcon(ToolbarIcons.SAVE);
+ jButtonSave.setToolTipText("Save...");
+ jButtonSave.setFocusable(false);
+ jButtonSave.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonSave.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonSaveActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonSave);
+
+ jButtonCut.setIcon(ToolbarIcons.CUT);
+ jButtonCut.setToolTipText("Cut");
+ jButtonCut.setFocusable(false);
+ jButtonCut.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonCut.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonCutActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonCut);
+
+ jButtonCopy.setIcon(ToolbarIcons.COPY);
+ jButtonCopy.setToolTipText("Copy");
+ jButtonCopy.setFocusable(false);
+ jButtonCopy.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonCopy.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonCopyActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonCopy);
+
+ jButtonPaste.setIcon(ToolbarIcons.PASTE);
+ jButtonPaste.setToolTipText("Paste");
+ jButtonPaste.setFocusable(false);
+ jButtonPaste.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonPaste.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonPasteActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonPaste);
+
+ jButtonDelete.setIcon(ToolbarIcons.DELETE);
+ jButtonDelete.setToolTipText("Delete");
+ jButtonDelete.setFocusable(false);
+ jButtonDelete.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonDelete.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonDeleteActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonDelete);
+
+ jButtonPrint.setIcon(ToolbarIcons.PRINT);
+ jButtonPrint.setToolTipText("Print");
+ jButtonPrint.setFocusable(false);
+ jButtonPrint.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonPrint.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonPrintActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonPrint);
+
+ jButtonExit.setIcon(ToolbarIcons.CLOSE);
+ jButtonExit.setToolTipText("Exit");
+ jButtonExit.setFocusable(false);
+ jButtonExit.setPreferredSize(new java.awt.Dimension(24, 24));
+ jButtonExit.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonExitActionPerformed(evt);
+ }
+ });
+
+ jToolBar.add(jButtonExit);
+
+ getContentPane().add(jToolBar, java.awt.BorderLayout.NORTH);
+
+ jSplitPaneBody.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
+ jSplitPaneBody.setOneTouchExpandable(true);
+ jSplitPaneIO.setOneTouchExpandable(true);
+ jSplitPaneSequences.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
+ jSplitPaneSequences.setOneTouchExpandable(true);
+ jPanelSequence1.setLayout(new java.awt.BorderLayout());
+
+ jScrollPaneSequence1.setPreferredSize(new java.awt.Dimension(400, 50));
+ jTextAreaSequence1.setFont(new java.awt.Font("DialogInput", 0, 12));
+ jTextAreaSequence1.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextAreaSequence1FocusGained(evt);
+ }
+ });
+ jTextAreaSequence1.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent evt) {
+ jTextAreaSequence1MouseClicked(evt);
+ }
+ });
+ jTextAreaSequence1.addCaretListener(new javax.swing.event.CaretListener() {
+ public void caretUpdate(javax.swing.event.CaretEvent evt) {
+ jTextAreaSequence1CaretUpdate(evt);
+ }
+ });
+
+ jScrollPaneSequence1.setViewportView(jTextAreaSequence1);
+
+ jPanelSequence1.add(jScrollPaneSequence1, java.awt.BorderLayout.CENTER);
+
+ jRadioButtonSequence1.setMnemonic('1');
+ jRadioButtonSequence1.setText("Sequence #1");
+ jRadioButtonSequence1.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jRadioButtonSequence1ActionPerformed(evt);
+ }
+ });
+
+ jPanelSequence1.add(jRadioButtonSequence1, java.awt.BorderLayout.NORTH);
+
+ jSplitPaneSequences.setTopComponent(jPanelSequence1);
+
+ jPanelSequence2.setLayout(new java.awt.BorderLayout());
+
+ jScrollPaneSequence2.setPreferredSize(new java.awt.Dimension(400, 50));
+ jTextAreaSequence2.setFont(new java.awt.Font("DialogInput", 0, 12));
+ jTextAreaSequence2.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextAreaSequence2FocusGained(evt);
+ }
+ });
+ jTextAreaSequence2.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent evt) {
+ jTextAreaSequence2MouseClicked(evt);
+ }
+ });
+ jTextAreaSequence2.addCaretListener(new javax.swing.event.CaretListener() {
+ public void caretUpdate(javax.swing.event.CaretEvent evt) {
+ jTextAreaSequence2CaretUpdate(evt);
+ }
+ });
+
+ jScrollPaneSequence2.setViewportView(jTextAreaSequence2);
+
+ jPanelSequence2.add(jScrollPaneSequence2, java.awt.BorderLayout.CENTER);
+
+ jRadioButtonSequence2.setMnemonic('2');
+ jRadioButtonSequence2.setText("Sequence #2");
+ jRadioButtonSequence2.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jRadioButtonSequence2ActionPerformed(evt);
+ }
+ });
+
+ jPanelSequence2.add(jRadioButtonSequence2, java.awt.BorderLayout.NORTH);
+
+ jSplitPaneSequences.setBottomComponent(jPanelSequence2);
+
+ jSplitPaneIO.setLeftComponent(jSplitPaneSequences);
+
+ jPanelAlignment.setLayout(new java.awt.BorderLayout());
+
+ jRadioButtonAlignment.setMnemonic('A');
+ jRadioButtonAlignment.setText("Alignment");
+ jRadioButtonAlignment.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jRadioButtonAlignmentActionPerformed(evt);
+ }
+ });
+
+ jPanelAlignment.add(jRadioButtonAlignment, java.awt.BorderLayout.NORTH);
+
+ jScrollPaneAlignment.setPreferredSize(new java.awt.Dimension(400, 50));
+ jTextAreaAlignment.setEditable(false);
+ jTextAreaAlignment.setFont(new java.awt.Font("DialogInput", 0, 12));
+ jTextAreaAlignment.setTabSize(0);
+ jTextAreaAlignment.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextAreaAlignmentFocusGained(evt);
+ }
+ });
+ jTextAreaAlignment.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent evt) {
+ jTextAreaAlignmentMouseClicked(evt);
+ }
+ });
+ jTextAreaAlignment.addCaretListener(new javax.swing.event.CaretListener() {
+ public void caretUpdate(javax.swing.event.CaretEvent evt) {
+ jTextAreaAlignmentCaretUpdate(evt);
+ }
+ });
+
+ jScrollPaneAlignment.setViewportView(jTextAreaAlignment);
+
+ jPanelAlignment.add(jScrollPaneAlignment, java.awt.BorderLayout.CENTER);
+
+ jSplitPaneIO.setRightComponent(jPanelAlignment);
+
+ jSplitPaneBody.setTopComponent(jSplitPaneIO);
+
+ jPanelConsole.setLayout(new java.awt.BorderLayout());
+
+ jRadioButtonConsole.setMnemonic('C');
+ jRadioButtonConsole.setText("Console");
+ jRadioButtonConsole.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jRadioButtonConsoleActionPerformed(evt);
+ }
+ });
+
+ jPanelConsole.add(jRadioButtonConsole, java.awt.BorderLayout.NORTH);
+
+ jScrollPaneConsole.setPreferredSize(new java.awt.Dimension(400, 50));
+ jTextPaneConsole.setEditable(false);
+ jTextPaneConsole.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextPaneConsoleFocusGained(evt);
+ }
+ });
+ jTextPaneConsole.addMouseListener(new java.awt.event.MouseAdapter() {
+ public void mouseClicked(java.awt.event.MouseEvent evt) {
+ jTextPaneConsoleMouseClicked(evt);
+ }
+ });
+ jTextPaneConsole.addCaretListener(new javax.swing.event.CaretListener() {
+ public void caretUpdate(javax.swing.event.CaretEvent evt) {
+ jTextPaneConsoleCaretUpdate(evt);
+ }
+ });
+
+ jScrollPaneConsole.setViewportView(jTextPaneConsole);
+
+ jPanelConsole.add(jScrollPaneConsole, java.awt.BorderLayout.CENTER);
+
+ jSplitPaneBody.setBottomComponent(jPanelConsole);
+
+ getContentPane().add(jSplitPaneBody, java.awt.BorderLayout.CENTER);
+
+ jPanelControls.setLayout(new java.awt.GridLayout(1, 0));
+
+ jPanelControls.setAutoscrolls(true);
+ jLabelScoringMatrix.setDisplayedMnemonic('M');
+ jLabelScoringMatrix.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ jLabelScoringMatrix.setLabelFor(jComboBoxScoringMatrix);
+ jLabelScoringMatrix.setText("Matrix");
+ jPanelScoringMatrix.add(jLabelScoringMatrix);
+
+ jComboBoxScoringMatrix.setToolTipText("Scoring matrix");
+ jComboBoxScoringMatrix.setPrototypeDisplayValue("BLOSUMXXX");
+ jPanelScoringMatrix.add(jComboBoxScoringMatrix);
+
+ jPanelControls.add(jPanelScoringMatrix);
+
+ jLabelOpenGapPenalty.setDisplayedMnemonic('O');
+ jLabelOpenGapPenalty.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ jLabelOpenGapPenalty.setLabelFor(jFormattedTextFieldGapOpen);
+ jLabelOpenGapPenalty.setText("Open");
+ jPanelGapOpen.add(jLabelOpenGapPenalty);
+
+ jFormattedTextFieldGapOpen.setColumns(3);
+ jFormattedTextFieldGapOpen.setToolTipText("Gap open penalty");
+ jPanelGapOpen.add(jFormattedTextFieldGapOpen);
+
+ jPanelControls.add(jPanelGapOpen);
+
+ jLabelExtendGapPenalty.setDisplayedMnemonic('E');
+ jLabelExtendGapPenalty.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
+ jLabelExtendGapPenalty.setLabelFor(jFormattedTextFieldGapExtend);
+ jLabelExtendGapPenalty.setText("Extend");
+ jPanelGapExtend.add(jLabelExtendGapPenalty);
+
+ jFormattedTextFieldGapExtend.setColumns(3);
+ jFormattedTextFieldGapExtend.setToolTipText("Gap extend penalty");
+ jPanelGapExtend.add(jFormattedTextFieldGapExtend);
+
+ jPanelControls.add(jPanelGapExtend);
+
+ jLabelOutputFormat.setDisplayedMnemonic('F');
+ jLabelOutputFormat.setLabelFor(jComboBoxOutputFormat);
+ jLabelOutputFormat.setText("Format");
+ jPanelOutputFormat.add(jLabelOutputFormat);
+
+ jComboBoxOutputFormat.setToolTipText("Alignment output format");
+ jComboBoxOutputFormat.setOpaque(false);
+ jPanelOutputFormat.add(jComboBoxOutputFormat);
+
+ jPanelControls.add(jPanelOutputFormat);
+
+ jButtonGo.setMnemonic('G');
+ jButtonGo.setText("Go");
+ jButtonGo.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jButtonGoActionPerformed(evt);
+ }
+ });
+
+ jPanelGo.add(jButtonGo);
+
+ jPanelControls.add(jPanelGo);
+
+ getContentPane().add(jPanelControls, java.awt.BorderLayout.SOUTH);
+
+ jMenuFile.setMnemonic('F');
+ jMenuFile.setText("File");
+ jMenuItemFileOpen.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemFileOpen.setIcon(ToolbarIcons.OPEN);
+ jMenuItemFileOpen.setMnemonic('O');
+ jMenuItemFileOpen.setText("Open...");
+ jMenuItemFileOpen.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemFileOpenActionPerformed(evt);
+ }
+ });
+
+ jMenuFile.add(jMenuItemFileOpen);
+
+ jMenuItemFileLoadSequence1.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_1, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemFileLoadSequence1.setIcon(ToolbarIcons.OPEN);
+ jMenuItemFileLoadSequence1.setMnemonic('1');
+ jMenuItemFileLoadSequence1.setText("Load sequence #1...");
+ jMenuItemFileLoadSequence1.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemFileLoadSequence1ActionPerformed(evt);
+ }
+ });
+
+ jMenuFile.add(jMenuItemFileLoadSequence1);
+
+ jMenuItemFileLoadSequence2.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_2, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemFileLoadSequence2.setIcon(ToolbarIcons.OPEN);
+ jMenuItemFileLoadSequence2.setMnemonic('2');
+ jMenuItemFileLoadSequence2.setText("Load sequence #2...");
+ jMenuItemFileLoadSequence2.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemFileLoadSequence2ActionPerformed(evt);
+ }
+ });
+
+ jMenuFile.add(jMenuItemFileLoadSequence2);
+
+ jMenuItemFileLoadMatrix.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_M, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemFileLoadMatrix.setIcon(ToolbarIcons.OPEN);
+ jMenuItemFileLoadMatrix.setMnemonic('M');
+ jMenuItemFileLoadMatrix.setText("Load scoring matrix...");
+ jMenuItemFileLoadMatrix.setToolTipText("Load user-defined scoring matrix from file system");
+ jMenuItemFileLoadMatrix.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemFileLoadMatrixActionPerformed(evt);
+ }
+ });
+
+ jMenuFile.add(jMenuItemFileLoadMatrix);
+
+ jMenuFile.add(jSeparatorFile);
+
+ jMenuItemFileExit.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.ALT_MASK));
+ jMenuItemFileExit.setIcon(ToolbarIcons.CLOSE);
+ jMenuItemFileExit.setMnemonic('X');
+ jMenuItemFileExit.setText("Exit");
+ jMenuItemFileExit.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemFileExitActionPerformed(evt);
+ }
+ });
+
+ jMenuFile.add(jMenuItemFileExit);
+
+ jMenuItemFilePrint.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemFilePrint.setIcon(ToolbarIcons.PRINT);
+ jMenuItemFilePrint.setText("Print...");
+ jMenuItemFilePrint.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemFilePrintActionPerformed(evt);
+ }
+ });
+
+ jMenuFile.add(jMenuItemFilePrint);
+
+ jMenuBar.add(jMenuFile);
+
+ jMenuEdit.setMnemonic('E');
+ jMenuEdit.setText("Edit");
+ jMenuItemEditCut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemEditCut.setIcon(ToolbarIcons.CUT);
+ jMenuItemEditCut.setMnemonic('t');
+ jMenuItemEditCut.setText("Cut");
+ jMenuItemEditCut.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemEditCutActionPerformed(evt);
+ }
+ });
+
+ jMenuEdit.add(jMenuItemEditCut);
+
+ jMenuItemEditCopy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemEditCopy.setIcon(ToolbarIcons.COPY);
+ jMenuItemEditCopy.setMnemonic('C');
+ jMenuItemEditCopy.setText("Copy");
+ jMenuItemEditCopy.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemEditCopyActionPerformed(evt);
+ }
+ });
+
+ jMenuEdit.add(jMenuItemEditCopy);
+
+ jMenuItemEditPaste.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemEditPaste.setIcon(ToolbarIcons.PASTE);
+ jMenuItemEditPaste.setMnemonic('P');
+ jMenuItemEditPaste.setText("Paste");
+ jMenuItemEditPaste.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemEditPasteActionPerformed(evt);
+ }
+ });
+
+ jMenuEdit.add(jMenuItemEditPaste);
+
+ jMenuItemEditDelete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0));
+ jMenuItemEditDelete.setIcon(ToolbarIcons.DELETE);
+ jMenuItemEditDelete.setMnemonic('D');
+ jMenuItemEditDelete.setText("Delete");
+ jMenuItemEditDelete.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemEditDeleteActionPerformed(evt);
+ }
+ });
+
+ jMenuEdit.add(jMenuItemEditDelete);
+
+ jMenuItemEditSelectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK));
+ jMenuItemEditSelectAll.setMnemonic('A');
+ jMenuItemEditSelectAll.setText("Select All");
+ jMenuItemEditSelectAll.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemEditSelectAllActionPerformed(evt);
+ }
+ });
+
+ jMenuEdit.add(jMenuItemEditSelectAll);
+
+ jMenuBar.add(jMenuEdit);
+
+ jMenuTools.setMnemonic('T');
+ jMenuTools.setText("Tools");
+ jMenuItemToolsRunExample.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F5, 0));
+ jMenuItemToolsRunExample.setMnemonic('E');
+ jMenuItemToolsRunExample.setText("Example");
+ jMenuItemToolsRunExample.setToolTipText("Aligns P53 human and P53 mouse");
+ jMenuItemToolsRunExample.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemToolsRunExampleActionPerformed(evt);
+ }
+ });
+
+ jMenuTools.add(jMenuItemToolsRunExample);
+
+ jMenuBar.add(jMenuTools);
+
+ jMenuHelp.setMnemonic('H');
+ jMenuHelp.setText("Help");
+ jMenuItemAbout.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0));
+ jMenuItemAbout.setIcon(ToolbarIcons.ABOUT);
+ jMenuItemAbout.setMnemonic('A');
+ jMenuItemAbout.setText("About...");
+ jMenuItemAbout.addActionListener(new java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ jMenuItemAboutActionPerformed(evt);
+ }
+ });
+
+ jMenuHelp.add(jMenuItemAbout);
+
+ jMenuBar.add(jMenuHelp);
+
+ setJMenuBar(jMenuBar);
+
+ pack();
+ }//GEN-END:initComponents
+
+ private void jPopupPrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupPrintActionPerformed
+ print();
+ }//GEN-LAST:event_jPopupPrintActionPerformed
+
+ private void jMenuItemToolsRunExampleActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemToolsRunExampleActionPerformed
+ try {
+ logger.info("Running the example...");
+ jTextAreaSequence1.setText(Example.loadP53Human());
+ jTextAreaSequence2.setText(Example.loadP53Mouse());
+ align();
+ jTextAreaAlignment.requestFocus();
+ logger.info("Finished running the example...");
+ } catch (Exception e) {
+ logger.log(Level.SEVERE, "Failed running the example: " + e.getMessage(), e);
+ }
+
+ }//GEN-LAST:event_jMenuItemToolsRunExampleActionPerformed
+
+ private void jMenuItemFilePrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFilePrintActionPerformed
+ print();
+ }//GEN-LAST:event_jMenuItemFilePrintActionPerformed
+
+ private void jButtonPrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonPrintActionPerformed
+ print();
+ }//GEN-LAST:event_jButtonPrintActionPerformed
+
+ private void jTextPaneConsoleCaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextPaneConsoleCaretUpdate
+ handleCaretUpdateEvent(evt);
+ }//GEN-LAST:event_jTextPaneConsoleCaretUpdate
+
+ private void jTextPaneConsoleMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextPaneConsoleMouseClicked
+ jTextPaneConsole.requestFocus();
+ if (evt.getButton() == MouseEvent.BUTTON3) {
+ jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
+ }
+ }//GEN-LAST:event_jTextPaneConsoleMouseClicked
+
+ private void jTextPaneConsoleFocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextPaneConsoleFocusGained
+ currentTextComponent = jTextPaneConsole;
+ jRadioButtonConsole.setSelected(true);
+ handleMoveToTextComponent();
+ }//GEN-LAST:event_jTextPaneConsoleFocusGained
+
+ private void jRadioButtonConsoleActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonConsoleActionPerformed
+ jTextPaneConsole.requestFocus();
+ }//GEN-LAST:event_jRadioButtonConsoleActionPerformed
+
+ private void jTextAreaAlignmentFocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentFocusGained
+ currentTextComponent = jTextAreaAlignment;
+ jRadioButtonAlignment.setSelected(true);
+ handleMoveToTextComponent();
+ }//GEN-LAST:event_jTextAreaAlignmentFocusGained
+
+ private void jTextAreaSequence2FocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaSequence2FocusGained
+ currentTextComponent = jTextAreaSequence2;
+ jRadioButtonSequence2.setSelected(true);
+ handleMoveToTextComponent();
+ }//GEN-LAST:event_jTextAreaSequence2FocusGained
+
+ private void jTextAreaSequence1FocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaSequence1FocusGained
+ currentTextComponent = jTextAreaSequence1;
+ jRadioButtonSequence1.setSelected(true);
+ handleMoveToTextComponent();
+ }//GEN-LAST:event_jTextAreaSequence1FocusGained
+
+ private void jRadioButtonAlignmentActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonAlignmentActionPerformed
+ jTextAreaAlignment.requestFocus();
+ }//GEN-LAST:event_jRadioButtonAlignmentActionPerformed
+
+ private void jRadioButtonSequence2ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonSequence2ActionPerformed
+ jTextAreaSequence2.requestFocus();
+ }//GEN-LAST:event_jRadioButtonSequence2ActionPerformed
+
+ private void jRadioButtonSequence1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonSequence1ActionPerformed
+ jTextAreaSequence1.requestFocus();
+ }//GEN-LAST:event_jRadioButtonSequence1ActionPerformed
+
+ private void jMenuItemEditCopyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditCopyActionPerformed
+ copy();
+ }//GEN-LAST:event_jMenuItemEditCopyActionPerformed
+
+ private void jMenuItemEditDeleteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditDeleteActionPerformed
+ delete();
+ }//GEN-LAST:event_jMenuItemEditDeleteActionPerformed
+
+ private void jMenuItemEditPasteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditPasteActionPerformed
+ paste();
+ }//GEN-LAST:event_jMenuItemEditPasteActionPerformed
+
+ private void jMenuItemFileOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileOpenActionPerformed
+ loadFileToTextArea("", currentTextComponent);
+ }//GEN-LAST:event_jMenuItemFileOpenActionPerformed
+
+ private void jMenuItemEditCutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditCutActionPerformed
+ cut();
+ }//GEN-LAST:event_jMenuItemEditCutActionPerformed
+
+ private void jMenuItemEditSelectAllActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditSelectAllActionPerformed
+ selectAll();
+ }//GEN-LAST:event_jMenuItemEditSelectAllActionPerformed
+
+ private void jTextAreaSequence2MouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextAreaSequence2MouseClicked
+ jTextAreaSequence2.requestFocus();
+ if (evt.getButton() == MouseEvent.BUTTON3) {
+ jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
+ }
+ }//GEN-LAST:event_jTextAreaSequence2MouseClicked
+
+ private void jTextAreaSequence2CaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextAreaSequence2CaretUpdate
+ handleCaretUpdateEvent(evt);
+ }//GEN-LAST:event_jTextAreaSequence2CaretUpdate
+
+ private void jButtonExitActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonExitActionPerformed
+ exitForm(null);
+ }//GEN-LAST:event_jButtonExitActionPerformed
+
+ private void jButtonGoActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonGoActionPerformed
+ align();
+ }//GEN-LAST:event_jButtonGoActionPerformed
+
+ private void jMenuItemFileLoadSequence2ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadSequence2ActionPerformed
+ loadFileToTextArea("sequence #2", jTextAreaSequence2);
+ }//GEN-LAST:event_jMenuItemFileLoadSequence2ActionPerformed
+
+ private void jMenuItemFileLoadSequence1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadSequence1ActionPerformed
+ loadFileToTextArea("sequence #1", jTextAreaSequence1);
+ }//GEN-LAST:event_jMenuItemFileLoadSequence1ActionPerformed
+
+ private void jMenuItemFileLoadMatrixActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadMatrixActionPerformed
+ NamedInputStream selectedInputStream = null;
+ try {
+ logger.info("Loading scoring matrix...");
+ selectedInputStream = FileChooserFactory.getFileChooser().open();
+ if (selectedInputStream != null) {
+ Matrix matrix = MatrixLoader.load(selectedInputStream);
+
+ // Put the loaded matrix in the matrices hashmap
+ matrices.put(selectedInputStream.getName(), matrix);
+
+ boolean found = false;
+ int index = 0;
+ int count = jComboBoxScoringMatrix.getItemCount();
+ while (index < count && !found) {
+ if (((String)jComboBoxScoringMatrix.getItemAt(index)).equalsIgnoreCase(selectedInputStream.getName())) {
+ found = true;
+ } else {
+ index++;
+ }
+ }
+ if (!found) {
+ // Add the loaded matrix to the scoring matrices dropdown menu
+ jComboBoxScoringMatrix.addItem(selectedInputStream.getName());
+ index = jComboBoxScoringMatrix.getItemCount()-1;
+ }
+ // Set the selected item to the new loaded matrix
+ jComboBoxScoringMatrix.setSelectedIndex(index);
+
+ logger.info("Finished loading scoring matrix");
+ } else {
+ logger.info("Canceled loading scoring matrix");
+ }
+ } catch (Exception e) {
+ String message = "Failed loading scoring matrix: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ showErrorMessage(message);
+ } finally {
+ if (selectedInputStream != null) {
+ try {
+ selectedInputStream.getInputStream().close();
+ } catch(Exception e) {
+ logger.log(Level.WARNING, "Failed closing input stream: " + e.getMessage(), e);
+ }
+ }
+ }
+ }//GEN-LAST:event_jMenuItemFileLoadMatrixActionPerformed
+
+ private void jTextAreaAlignmentMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentMouseClicked
+ jTextAreaAlignment.requestFocus();
+ if (evt.getButton() == MouseEvent.BUTTON3) {
+ jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
+ }
+ }//GEN-LAST:event_jTextAreaAlignmentMouseClicked
+
+ private void jPopupSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupSaveActionPerformed
+ saveTextAreaToFile((JTextArea) jPopup.getInvoker());
+ }//GEN-LAST:event_jPopupSaveActionPerformed
+
+ private void jButtonSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonSaveActionPerformed
+ saveTextAreaToFile(currentTextComponent);
+ }//GEN-LAST:event_jButtonSaveActionPerformed
+
+ private void jTextAreaAlignmentCaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentCaretUpdate
+ handleCaretUpdateEvent(evt);
+ }//GEN-LAST:event_jTextAreaAlignmentCaretUpdate
+
+ private void jPopupOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupOpenActionPerformed
+ loadFileToTextArea("", (JTextArea) jPopup.getInvoker());
+ }//GEN-LAST:event_jPopupOpenActionPerformed
+
+ private void jPopupSelectAllActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupSelectAllActionPerformed
+ selectAll();
+ }//GEN-LAST:event_jPopupSelectAllActionPerformed
+
+ private void jPopupDeleteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupDeleteActionPerformed
+ delete();
+ }//GEN-LAST:event_jPopupDeleteActionPerformed
+
+ private void jPopupPasteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupPasteActionPerformed
+ paste();
+ }//GEN-LAST:event_jPopupPasteActionPerformed
+
+ private void jPopupCopyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupCopyActionPerformed
+ copy();
+ }//GEN-LAST:event_jPopupCopyActionPerformed
+
+ private void jPopupCutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupCutActionPerformed
+ cut();
+ }//GEN-LAST:event_jPopupCutActionPerformed
+
+ private void jTextAreaSequence1CaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextAreaSequence1CaretUpdate
+ handleCaretUpdateEvent(evt);
+ }//GEN-LAST:event_jTextAreaSequence1CaretUpdate
+
+ private void jButtonDeleteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonDeleteActionPerformed
+ delete();
+ }//GEN-LAST:event_jButtonDeleteActionPerformed
+
+ private void jButtonPasteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonPasteActionPerformed
+ paste();
+ }//GEN-LAST:event_jButtonPasteActionPerformed
+
+ private void jButtonCopyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonCopyActionPerformed
+ copy();
+ }//GEN-LAST:event_jButtonCopyActionPerformed
+
+ private void jButtonCutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonCutActionPerformed
+ cut();
+ }//GEN-LAST:event_jButtonCutActionPerformed
+
+ private void jButtonOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonOpenActionPerformed
+ loadFileToTextArea("", currentTextComponent);
+ }//GEN-LAST:event_jButtonOpenActionPerformed
+
+ private void jTextAreaSequence1MouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextAreaSequence1MouseClicked
+ jTextAreaSequence1.requestFocus();
+ if (evt.getButton() == MouseEvent.BUTTON3) {
+ jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
+ }
+ }//GEN-LAST:event_jTextAreaSequence1MouseClicked
+
+ private void jMenuItemAboutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemAboutActionPerformed
+ String message = "JAligner <http://jaligner.sf.net>"
+ + Commons.getLineSeparator() + Commons.getLineSeparator()
+ + "Open source Java implementation"
+ + Commons.getLineSeparator()
+ + "of the Smith-Waterman algorithm"
+ + Commons.getLineSeparator()
+ + "for biological sequence alignment."
+ + Commons.getLineSeparator() + Commons.getLineSeparator()
+ + "Build: " + Commons.getCurrentRelease()
+ + Commons.getLineSeparator() + Commons.getLineSeparator()
+ + "By: Ahmed Moustafa <ahmed at users.sf.net>";
+ JOptionPane.showMessageDialog(this, message, "About JAligner",
+ JOptionPane.INFORMATION_MESSAGE);
+ }//GEN-LAST:event_jMenuItemAboutActionPerformed
+
+ private void jMenuItemFileExitActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileExitActionPerformed
+ exitForm(null);
+ }//GEN-LAST:event_jMenuItemFileExitActionPerformed
+
+ /** Exit the Application */
+ private void exitForm(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_exitForm
+ logger.info("Quitting...");
+ if (JOptionPane.showConfirmDialog(this, "Are you sure you want to exit JAligner?", "JAligner - confirmation", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
+ logger.info("Thank you for using JAligner!");
+ System.exit(0);
+ } else {
+ logger.info("Canceled quitting");
+ currentTextComponent.requestFocus();
+ }
+ }//GEN-LAST:event_exitForm
+
+ // Variables declaration - do not modify//GEN-BEGIN:variables
+ private javax.swing.ButtonGroup buttonGroupSequences;
+ private javax.swing.JButton jButtonCopy;
+ private javax.swing.JButton jButtonCut;
+ private javax.swing.JButton jButtonDelete;
+ private javax.swing.JButton jButtonExit;
+ private javax.swing.JButton jButtonGo;
+ private javax.swing.JButton jButtonOpen;
+ private javax.swing.JButton jButtonPaste;
+ private javax.swing.JButton jButtonPrint;
+ private javax.swing.JButton jButtonSave;
+ private javax.swing.JComboBox jComboBoxOutputFormat;
+ private javax.swing.JComboBox jComboBoxScoringMatrix;
+ private javax.swing.JFormattedTextField jFormattedTextFieldGapExtend;
+ private javax.swing.JFormattedTextField jFormattedTextFieldGapOpen;
+ private javax.swing.JLabel jLabelExtendGapPenalty;
+ private javax.swing.JLabel jLabelOpenGapPenalty;
+ private javax.swing.JLabel jLabelOutputFormat;
+ private javax.swing.JLabel jLabelScoringMatrix;
+ private javax.swing.JMenuBar jMenuBar;
+ private javax.swing.JMenu jMenuEdit;
+ private javax.swing.JMenu jMenuFile;
+ private javax.swing.JMenu jMenuHelp;
+ private javax.swing.JMenuItem jMenuItemAbout;
+ private javax.swing.JMenuItem jMenuItemEditCopy;
+ private javax.swing.JMenuItem jMenuItemEditCut;
+ private javax.swing.JMenuItem jMenuItemEditDelete;
+ private javax.swing.JMenuItem jMenuItemEditPaste;
+ private javax.swing.JMenuItem jMenuItemEditSelectAll;
+ private javax.swing.JMenuItem jMenuItemFileExit;
+ private javax.swing.JMenuItem jMenuItemFileLoadMatrix;
+ private javax.swing.JMenuItem jMenuItemFileLoadSequence1;
+ private javax.swing.JMenuItem jMenuItemFileLoadSequence2;
+ private javax.swing.JMenuItem jMenuItemFileOpen;
+ private javax.swing.JMenuItem jMenuItemFilePrint;
+ private javax.swing.JMenuItem jMenuItemToolsRunExample;
+ private javax.swing.JMenu jMenuTools;
+ private javax.swing.JPanel jPanelAlignment;
+ private javax.swing.JPanel jPanelConsole;
+ private javax.swing.JPanel jPanelControls;
+ private javax.swing.JPanel jPanelGapExtend;
+ private javax.swing.JPanel jPanelGapOpen;
+ private javax.swing.JPanel jPanelGo;
+ private javax.swing.JPanel jPanelOutputFormat;
+ private javax.swing.JPanel jPanelScoringMatrix;
+ private javax.swing.JPanel jPanelSequence1;
+ private javax.swing.JPanel jPanelSequence2;
+ private javax.swing.JPopupMenu jPopup;
+ private javax.swing.JMenuItem jPopupCopy;
+ private javax.swing.JMenuItem jPopupCut;
+ private javax.swing.JMenuItem jPopupDelete;
+ private javax.swing.JMenuItem jPopupOpen;
+ private javax.swing.JMenuItem jPopupPaste;
+ private javax.swing.JMenuItem jPopupPrint;
+ private javax.swing.JMenuItem jPopupSave;
+ private javax.swing.JMenuItem jPopupSelectAll;
+ private javax.swing.JSeparator jPopupSeparator1;
+ private javax.swing.JSeparator jPopupSeparator2;
+ private javax.swing.JSeparator jPopupSeparator3;
+ private javax.swing.JRadioButton jRadioButtonAlignment;
+ private javax.swing.JRadioButton jRadioButtonConsole;
+ private javax.swing.JRadioButton jRadioButtonSequence1;
+ private javax.swing.JRadioButton jRadioButtonSequence2;
+ private javax.swing.JScrollPane jScrollPaneAlignment;
+ private javax.swing.JScrollPane jScrollPaneConsole;
+ private javax.swing.JScrollPane jScrollPaneSequence1;
+ private javax.swing.JScrollPane jScrollPaneSequence2;
+ private javax.swing.JSeparator jSeparatorFile;
+ private javax.swing.JSplitPane jSplitPaneBody;
+ private javax.swing.JSplitPane jSplitPaneIO;
+ private javax.swing.JSplitPane jSplitPaneSequences;
+ private javax.swing.JTextArea jTextAreaAlignment;
+ private javax.swing.JTextArea jTextAreaSequence1;
+ private javax.swing.JTextArea jTextAreaSequence2;
+ private javax.swing.JTextPane jTextPaneConsole;
+ private javax.swing.JToolBar jToolBar;
+ // End of variables declaration//GEN-END:variables
+
+ /**
+ * Populates a combobox with an array of strings and selects the default
+ * @param combobox combobox to be populated
+ * @param items array of strings to be added to the combobox
+ * @param selected the default selected item
+ */
+ private void populateComboBox(JComboBox combobox, String[] items, String selected) {
+ for (int i = 0; i < items.length; i++) {
+ combobox.addItem(items[i]);
+ if (items[i].equals(selected)) {
+ combobox.setSelectedIndex(i);
+ }
+ }
+ }
+
+ /**
+ * Populates a combobox with an array of strings and selects the default
+ * @param combobox combobox to be populated
+ * @param items array of strings to be added to the combobox
+ * @param selected the default selected item
+ */
+ private void populateComboBox(JComboBox combobox, Collection items, String selected) {
+ String item;
+ Iterator i = items.iterator();
+ int index = 0;
+ while (i.hasNext()) {
+ item = (String) i.next();
+ combobox.addItem(item);
+ if (item.equals(selected)) {
+ combobox.setSelectedIndex(index);
+ }
+ index++;
+ }
+ }
+
+ /**
+ * Displays an error message
+ * @param message the error message to be displayed
+ */
+ private void showErrorMessage(String message) {
+ JOptionPane.showMessageDialog(this, message, "JAligner - error message", JOptionPane.ERROR_MESSAGE);
+ }
+
+ /**
+ * Loads the contents of a selected file into a text component.
+ * @param id
+ * @param textComponent
+ */
+ private void loadFileToTextArea(String id, JTextComponent textComponent) {
+ logger.info("Loading " + id + "...");
+ try {
+ if (TextComponentUtil.open(textComponent)) {
+ textComponent.requestFocus();
+ textComponent.setCaretPosition(0);
+ logger.info("Finished loading " + id);
+ } else {
+ logger.info("Canceled loading " + id);
+ }
+ } catch (Exception e) {
+ String message = "Failed loading " + id + ": " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ showErrorMessage(message);
+ }
+ }
+
+ /**
+ * Saves a text component to a file.
+ * @param textComponent
+ */
+ private void saveTextAreaToFile(JTextComponent textComponent) {
+ try {
+ logger.info("Saving...");
+ if (TextComponentUtil.save(textComponent)) {
+ logger.info("Finished saving");
+ } else {
+ logger.info("Canceled saving");
+ }
+ } catch (Exception e) {
+ String message = "Failed saving: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ showErrorMessage(message);
+ }
+ }
+
+ /**
+ *
+ *
+ */
+ private void cut() {
+ TextComponentUtil.cut(currentTextComponent);
+ }
+
+ /**
+ *
+ *
+ */
+ private void copy() {
+ TextComponentUtil.copy(currentTextComponent);
+ }
+
+ /**
+ *
+ *
+ */
+ private void paste() {
+ TextComponentUtil.paste(currentTextComponent);
+ }
+
+ /**
+ *
+ *
+ */
+ private void delete() {
+ TextComponentUtil.delete(currentTextComponent);
+ }
+
+ /**
+ *
+ *
+ */
+ private void selectAll() {
+ TextComponentUtil.selectAll(currentTextComponent);
+ }
+
+ /**
+ * Prints the contents of a text component
+ *
+ */
+ private void print() {
+ try {
+ logger.info("Printing...");
+ TextComponentUtil.print(currentTextComponent);
+ logger.info("Finished printing.");
+ } catch (TextComponentUtilException textComponentUtilException) {
+ logger.log(Level.SEVERE, "Failed printing: " + textComponentUtilException.getMessage(), textComponentUtilException);
+ }
+ }
+
+ /**
+ * Implements insertUpdate of {@link DocumentListener}
+ */
+ public void insertUpdate(DocumentEvent e) {
+ if (e.getDocument() == currentTextComponent.getDocument()) {
+ setSaveControlsEnabled(true);
+ setSelectAllControlsEnabled(true);
+ setPrintControlsEnabled(true);
+ }
+ }
+
+ /**
+ * Implements removeUpdate of {@link DocumentListener}
+ */
+ public void removeUpdate(DocumentEvent e) {
+ if (e.getDocument() == currentTextComponent.getDocument()) {
+ if (e.getDocument().getLength() == 0) {
+ setSaveControlsEnabled(false);
+ setSelectAllControlsEnabled(false);
+ setPrintControlsEnabled(false);
+ }
+ }
+ }
+
+ /**
+ * Implements changedUpdate of {@link DocumentListener}
+ */
+ public void changedUpdate(DocumentEvent e) {}
+
+ /**
+ * Implements the notify method of the interface {@link ClipboardListener}
+ */
+ public void clipboardCheck(String clipboardContents) {
+ setPasteControlsEnabled(clipboardContents != null && currentTextComponent != null && currentTextComponent.isEditable());
+ }
+
+ /**
+ * Sets the status of the open controls
+ * @param enabled
+ */
+ private void setOpenControlsEnabled(boolean enabled) {
+ jMenuItemFileOpen.setEnabled(enabled);
+ jButtonOpen.setEnabled(enabled);
+ jPopupOpen.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the save controls
+ * @param enabled
+ */
+ private void setSaveControlsEnabled(boolean enabled) {
+ jButtonSave.setEnabled(enabled);
+ jPopupSave.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the cut controls
+ * @param enabled
+ */
+ private void setCutControlsEnabled(boolean enabled) {
+ jMenuItemEditCut.setEnabled(enabled);
+ jButtonCut.setEnabled(enabled);
+ jPopupCut.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the copy controls
+ * @param enabled
+ */
+ private void setCopyControlsEnabled(boolean enabled) {
+ jMenuItemEditCopy.setEnabled(enabled);
+ jButtonCopy.setEnabled(enabled);
+ jPopupCopy.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the paste controls
+ * @param enabled
+ */
+ private void setPasteControlsEnabled(boolean enabled) {
+ jMenuItemEditPaste.setEnabled(enabled);
+ jButtonPaste.setEnabled(enabled);
+ jPopupPaste.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the delete controls
+ * @param enabled
+ */
+ private void setDeleteControlsEnabled(boolean enabled) {
+ jMenuItemEditDelete.setEnabled(enabled);
+ jButtonDelete.setEnabled(enabled);
+ jPopupDelete.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the select all controls
+ * @param enabled
+ */
+ private void setSelectAllControlsEnabled(boolean enabled) {
+ jMenuItemEditSelectAll.setEnabled(enabled);
+ jPopupSelectAll.setEnabled(enabled);
+ }
+
+ /**
+ * Sets the status of the print controls
+ * @param enabled
+ */
+ private void setPrintControlsEnabled(boolean enabled) {
+ jButtonPrint.setEnabled(enabled);
+ jPopupPrint.setEnabled(enabled);
+ }
+
+ /**
+ *
+ * @param event
+ */
+ private void handleCaretUpdateEvent(CaretEvent event) {
+ if (event.getSource() == currentTextComponent) {
+ boolean enabled = event.getDot() != event.getMark();
+ // Read controls
+ setCopyControlsEnabled(enabled);
+
+ // Write controls
+ enabled &= currentTextComponent.isEditable();
+ setCutControlsEnabled(enabled);
+ setDeleteControlsEnabled(enabled);
+ }
+ }
+
+ /**
+ *
+ *
+ */
+ private void handleMoveToTextComponent( ) {
+ boolean enabled;
+
+ enabled = currentTextComponent.getSelectedText() != null;
+ setCopyControlsEnabled(enabled);
+
+ if (currentTextComponent.isEditable()) {
+ setOpenControlsEnabled(true);
+
+ setCutControlsEnabled(enabled);
+ setDeleteControlsEnabled(enabled);
+ } else {
+ setPasteControlsEnabled(false);
+
+ setOpenControlsEnabled(false);
+
+ setCutControlsEnabled(false);
+ setDeleteControlsEnabled(false);
+ }
+
+ enabled = currentTextComponent.getText().length() > 0;
+ setSaveControlsEnabled(enabled);
+ setSelectAllControlsEnabled(enabled);
+ setPrintControlsEnabled(enabled);
+
+ // Adjust background of the radio buttons
+ Enumeration buttons = buttonGroupSequences.getElements();
+ AbstractButton button = null;
+ while (buttons.hasMoreElements()) {
+ button = (AbstractButton) buttons.nextElement();
+ if (button.isSelected()) {
+ button.setForeground(Color.blue);
+ } else {
+ button.setForeground(Color.black);
+ }
+ }
+
+ }
+
+ /**
+ *
+ *
+ */
+ private void align() {
+ jTextAreaAlignment.setText("");
+
+ String matrixId = (String) jComboBoxScoringMatrix.getSelectedItem();
+ float open = ((Number)jFormattedTextFieldGapOpen.getValue()).floatValue();
+ float extend = ((Number)jFormattedTextFieldGapExtend.getValue()).floatValue();
+
+ Sequence sequence1 = null;
+ try {
+ logger.info("Processing sequence #1...");
+ sequence1 = SequenceParser.parse(jTextAreaSequence1.getText());
+ logger.info("Finished processing sequence #1");
+ } catch (Exception e) {
+ String message = "Failed parsing sequence #1: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ showErrorMessage(message);
+ jTextAreaSequence1.requestFocus();
+ return;
+ }
+
+ Sequence sequence2 = null;
+ try {
+ logger.info("Processing sequence #2...");
+ sequence2 = SequenceParser.parse(jTextAreaSequence2.getText());
+ logger.info("Finished processing sequence #2");
+ } catch (Exception e) {
+ String message = "Failed parsing sequence #2: " + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ showErrorMessage(message);
+ jTextAreaSequence2.requestFocus();
+ return;
+ }
+
+ logger.info("Aliging...");
+ try {
+ setCursor(new Cursor(Cursor.WAIT_CURSOR));
+
+ long start = System.currentTimeMillis();
+ Matrix matrix = null;
+ if (!matrices.containsKey(matrixId)) {
+ matrix = MatrixLoader.load(matrixId);
+ matrices.put(matrixId, matrix);
+ } else {
+ matrix = (Matrix) matrices.get(matrixId);
+ }
+ Alignment alignment = SmithWatermanGotoh.align(sequence1, sequence2, matrix, open, extend);
+ long end = System.currentTimeMillis();
+ logger.info("Finished aligning in " + (end - start) + " milliseconds");
+
+ StringBuffer buffer = new StringBuffer();
+
+ buffer.append(alignment.getSummary());
+ buffer.append(Commons.getLineSeparator());
+
+ String formatId = (String) jComboBoxOutputFormat.getSelectedItem();
+ String formattedAlignment = FormatFactory.getInstance().getFormat(formatId).format(alignment);
+ buffer.append(formattedAlignment);
+
+ jTextAreaAlignment.setText("");
+ jTextAreaAlignment.append(buffer.toString());
+ jTextAreaAlignment.setCaretPosition(0);
+ } catch (Error error) {
+ String message = "Failed aligning: " + error.getMessage();
+ logger.log(Level.SEVERE, message, error);
+ showErrorMessage(message);
+ } catch (Exception exception) {
+ String message = "Failed aligning: " + exception.getMessage();
+ logger.log(Level.SEVERE, message, exception);
+ showErrorMessage(message);
+ } finally {
+ setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ }
+
+ /**
+ *
+ * @param args
+ */
+ public static void main(String[] args) {
+ logger.info( Commons.getJAlignerInfo() );
+ new AlignWindow().setVisible(true);
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/ClipboardHandler.java b/src/jaligner/ui/clipboard/ClipboardHandler.java
new file mode 100644
index 0000000..e5020e7
--- /dev/null
+++ b/src/jaligner/ui/clipboard/ClipboardHandler.java
@@ -0,0 +1,42 @@
+/*
+ * $Id: ClipboardHandler.java,v 1.4 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.clipboard;
+
+/**
+ * Abstract class to handle setting and getting "text" contents of
+ * the system clipboard.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public interface ClipboardHandler {
+ /**
+ * Returns the contents of the system of the clipboard
+ *
+ * @return String
+ */
+ public String getContents();
+
+ /**
+ * Sets the contents of the system of the clipboard
+ *
+ * @param s the clipboard contents to set
+ */
+ public void setContents(String s);
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java b/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java
new file mode 100644
index 0000000..95859b7
--- /dev/null
+++ b/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java
@@ -0,0 +1,67 @@
+/*
+ * $Id: ClipboardHandlerAWT.java,v 1.3 2004/12/19 08:00:48 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.clipboard;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+
+/**
+ * Sets and gets the contents of the system clipboard.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class ClipboardHandlerAWT implements ClipboardHandler {
+ private static Logger logger = Logger.getLogger(ClipboardHandlerAWT.class.getName());
+
+ /**
+ * Gets the contents of the system clipboard
+ *
+ * @return The text contents of the system clipboard
+ */
+ public String getContents() {
+ String contents = null;
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable data = c.getContents(null);
+ if (data != null && data.isDataFlavorSupported(DataFlavor.stringFlavor)) {
+ try {
+ contents = ((String)(data.getTransferData(DataFlavor.stringFlavor)));
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting tranfer data: " + e.getMessage(), e);
+ }
+ }
+ return contents;
+ }
+
+ /**
+ * Sets the contents of the system clipboard
+ *
+ * @param s the clipboard contents to set
+ */
+ public void setContents(String s) {
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ c.setContents(new StringSelection(s), null);
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java b/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java
new file mode 100644
index 0000000..d8cbf4d
--- /dev/null
+++ b/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java
@@ -0,0 +1,56 @@
+/*
+ * $Id: ClipboardHandlerFactory.java,v 1.2 2004/11/30 05:10:29 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.clipboard;
+
+import jaligner.util.Commons;
+
+/**
+ * A factory for {@link jaligner.ui.clipboard.ClipboardHandler}.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class ClipboardHandlerFactory {
+ /**
+ * Instance of a concrete {@link ClipboardHandlerFactory}.
+ */
+ private static ClipboardHandler instance = null;
+
+ /**
+ * Constructor
+ */
+ private ClipboardHandlerFactory ( ) {
+ super();
+ }
+
+ /**
+ * Returns an instance of a concrete {@link ClipboardHandler}.
+ * @return Concrete {@link ClipboardHandler}.
+ */
+ public static ClipboardHandler getClipboardHandler( ) {
+ if (instance == null) {
+ if (Commons.isJnlp()) {
+ instance = new ClipboardHandlerJNLP();
+ } else {
+ instance = new ClipboardHandlerAWT();
+ }
+ }
+ return instance;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java b/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
new file mode 100644
index 0000000..e31ee47
--- /dev/null
+++ b/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
@@ -0,0 +1,71 @@
+/*
+ * $Id: ClipboardHandlerJNLP.java,v 1.3 2004/12/19 08:00:48 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.clipboard;
+
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.jnlp.ClipboardService;
+import javax.jnlp.ServiceManager;
+
+/**
+ * Sets and gets the contents of the system clipboard.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class ClipboardHandlerJNLP implements ClipboardHandler {
+ private static Logger logger = Logger.getLogger(ClipboardHandlerJNLP.class.getName());
+
+ /**
+ * Gets the contents of the system clipboard
+ *
+ * @return The text system clipboad contents
+ */
+ public String getContents() {
+ String contents = null;
+ try {
+ ClipboardService cs = (ClipboardService)ServiceManager.lookup(ClipboardService.class.getName());
+ Transferable data = cs.getContents();
+ if (data != null && data.isDataFlavorSupported(DataFlavor.stringFlavor)) {
+ contents = ((String)(data.getTransferData(DataFlavor.stringFlavor)));
+ }
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting the clipboard contents: " + e.getMessage(), e );
+ }
+ return contents;
+ }
+
+ /**
+ * Sets the contents of the system clipboard
+ *
+ * @param s clipboard contents to set
+ */
+ public void setContents(String s) {
+ try {
+ ClipboardService cs = (ClipboardService)ServiceManager.lookup(ClipboardService.class.getName());
+ cs.setContents(new StringSelection(s));
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed setting the clipboard contents: " + e.getMessage(), e );
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/ClipboardListener.java b/src/jaligner/ui/clipboard/ClipboardListener.java
new file mode 100644
index 0000000..915c64b
--- /dev/null
+++ b/src/jaligner/ui/clipboard/ClipboardListener.java
@@ -0,0 +1,35 @@
+/*
+ * $Id: ClipboardListener.java,v 1.5 2004/12/23 17:06:47 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.clipboard;
+
+/**
+ * Listener interface to get notified with the clipboard contents.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public interface ClipboardListener {
+
+ /**
+ * Notifies the listener with the current contents of the clipboard.
+ * @param contents The current contents of the clipboard
+ */
+ public void clipboardCheck (String contents);
+
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/ClipboardPoller.java b/src/jaligner/ui/clipboard/ClipboardPoller.java
new file mode 100644
index 0000000..0b4daf0
--- /dev/null
+++ b/src/jaligner/ui/clipboard/ClipboardPoller.java
@@ -0,0 +1,94 @@
+/*
+ * $Id: ClipboardPoller.java,v 1.5 2004/12/23 17:06:47 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.clipboard;
+
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Checks the system clipboard to notifies a listener with current contents.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class ClipboardPoller extends Thread {
+ /**
+ * Sleeping interval
+ */
+ private static final int SLEEPING_TIME_IN_MILLISECONDS = 1500;
+
+ /**
+ * Clipboard listener {@link ClipboardListener}
+ */
+ private ClipboardListener listener = null;
+
+ /**
+ * Running flag
+ */
+ private boolean running = false;
+
+ /**
+ * Logger
+ */
+ private Logger logger = null;
+
+ /**
+ * Constructor
+ * @param listener
+ */
+ public ClipboardPoller(ClipboardListener listener) {
+ logger = Logger.getLogger(this.getClass().getName());
+ this.listener = listener;
+ }
+
+ /**
+ * Runs the thread
+ */
+ public void run() {
+ logger.info("Started");
+ while (running) {
+ String contents = ClipboardHandlerFactory.getClipboardHandler().getContents();
+ listener.clipboardCheck(contents);
+ try {
+ Thread.sleep(SLEEPING_TIME_IN_MILLISECONDS);
+ } catch (Exception e){
+ logger.log(Level.SEVERE, "Failed sleeping: " + e.getMessage(), e);
+ running = false;
+ }
+ }
+ logger.info("Stopped");
+ }
+
+ /**
+ * Starts the thread
+ */
+ public void start() {
+ logger.info("Starting...");
+ if (!running) {
+ if (listener != null) {
+ running = true;
+ } else {
+ logger.warning("No listener");
+ }
+ } else {
+ logger.warning("Already started");
+ }
+ super.start();
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/clipboard/package.html b/src/jaligner/ui/clipboard/package.html
new file mode 100644
index 0000000..d3f3582
--- /dev/null
+++ b/src/jaligner/ui/clipboard/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.2 2004/12/10 06:41:24 ahmed Exp $--></head>
+<body bgcolor="white">
+Clipboard handling for JNLP and AWT.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/FileChooser.java b/src/jaligner/ui/filechooser/FileChooser.java
new file mode 100644
index 0000000..a7a1a5b
--- /dev/null
+++ b/src/jaligner/ui/filechooser/FileChooser.java
@@ -0,0 +1,73 @@
+/*
+ * $Id: FileChooser.java,v 1.10 2005/01/10 15:01:01 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.filechooser;
+
+import java.io.InputStream;
+
+/**
+ * Opens and saves files.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public abstract class FileChooser {
+ /**
+ * Buffer size while reading from or write to a file (4 KB)
+ */
+ public static final int BUFFER_SIZE = 4096;
+
+ private String userDir = null;
+
+ /**
+ * Shows a dialog to select a file
+ *
+ * @return InputStream
+ * @throws FileChooserException
+ */
+ public abstract NamedInputStream open() throws FileChooserException;
+
+ /**
+ * Saves an input stream to a file
+ *
+ * @param is
+ * @param fileName
+ * @return boolean
+ * @throws FileChooserException
+ */
+ public abstract boolean save(InputStream is, String fileName) throws FileChooserException;
+
+ /**
+ * Gets the current user working directory
+ * @return current working directory
+ */
+ public String getUserDirectory ( ) {
+ if (userDir == null) {
+ userDir = System.getProperty("user.home");
+ }
+ return userDir;
+ }
+
+ /**
+ * Sets the user working directory
+ * @param userDir The user directory to set
+ */
+ public void setUserDirectory (String userDir) {
+ this.userDir = userDir;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/FileChooserException.java b/src/jaligner/ui/filechooser/FileChooserException.java
new file mode 100644
index 0000000..3882735
--- /dev/null
+++ b/src/jaligner/ui/filechooser/FileChooserException.java
@@ -0,0 +1,40 @@
+/*
+ * $Id: FileChooserException.java,v 1.2 2005/04/14 14:44:43 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.filechooser;
+
+/**
+ * File chooser exception
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class FileChooserException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3258408434931086648L;
+
+ /**
+ * @param message
+ */
+ public FileChooserException(String message) {
+ super(message);
+ }
+}
diff --git a/src/jaligner/ui/filechooser/FileChooserFactory.java b/src/jaligner/ui/filechooser/FileChooserFactory.java
new file mode 100644
index 0000000..867db72
--- /dev/null
+++ b/src/jaligner/ui/filechooser/FileChooserFactory.java
@@ -0,0 +1,56 @@
+/*
+ * $Id: FileChooserFactory.java,v 1.3 2005/01/11 15:23:25 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.filechooser;
+
+import jaligner.util.Commons;
+
+/**
+ * A factory for {@link jaligner.ui.filechooser.FileChooser}.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class FileChooserFactory {
+ /**
+ * Instance of a concrete {@link FileChooser}.
+ */
+ private static FileChooser instance = null;
+
+ /**
+ * Constructor
+ */
+ private FileChooserFactory ( ) {
+ super();
+ }
+
+ /**
+ * Returns an instance of a concrete {@link FileChooser}.
+ * @return Concrete {@link FileChooser}.
+ */
+ public static FileChooser getFileChooser( ) {
+ if (instance == null) {
+ if (Commons.isJnlp()) {
+ instance = new FileChooserJNLP();
+ } else {
+ instance = new FileChooserTrusted();
+ }
+ }
+ return instance;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/FileChooserJNLP.java b/src/jaligner/ui/filechooser/FileChooserJNLP.java
new file mode 100644
index 0000000..d794034
--- /dev/null
+++ b/src/jaligner/ui/filechooser/FileChooserJNLP.java
@@ -0,0 +1,85 @@
+/*
+ * $Id: FileChooserJNLP.java,v 1.11 2005/01/10 15:01:01 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.filechooser;
+
+import java.io.InputStream;
+import java.util.logging.Logger;
+
+import javax.jnlp.FileContents;
+import javax.jnlp.FileOpenService;
+import javax.jnlp.FileSaveService;
+import javax.jnlp.ServiceManager;
+
+/**
+ * Opens and saves files.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class FileChooserJNLP extends FileChooser {
+ private static final Logger logger = Logger.getLogger(FileChooserJNLP.class.getName());
+
+ /**
+ * Shows a dialog to select a file.
+ *
+ * @return InputStream
+ * @throws FileChooserException
+ */
+ public NamedInputStream open() throws FileChooserException {
+ try {
+ FileOpenService fos = (FileOpenService) ServiceManager.lookup(FileOpenService.class.getName());
+ FileContents fc = null;
+ if ((fc = fos.openFileDialog(getUserDirectory(), null)) != null) {
+ logger.info("Loaded: " + fc.getName());
+ return new NamedInputStream(fc.getName(), fc.getInputStream());
+ } else {
+ return null;
+ }
+ } catch (Exception e) {
+ String message = "Failed open: " + e.getMessage();
+ logger.warning(message);
+ throw new FileChooserException(message);
+ }
+ }
+
+ /**
+ * Saves an input stream to a file.
+ *
+ * @param is
+ * @param fileName
+ * @return Boolean
+ * @throws FileChooserException
+ */
+ public boolean save(InputStream is, String fileName) throws FileChooserException {
+ try {
+ FileSaveService fss = (FileSaveService) ServiceManager.lookup(FileSaveService.class.getName());
+ FileContents fc = fss.saveFileDialog(getUserDirectory(), null, is, fileName);
+ if (fc != null) {
+ logger.info("Saved: " + fc.getName());
+ return true;
+ } else {
+ return false;
+ }
+ } catch (Exception e) {
+ String message = "Failed save: " + e.getMessage();
+ logger.warning(message);
+ throw new FileChooserException(message);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/FileChooserTrusted.java b/src/jaligner/ui/filechooser/FileChooserTrusted.java
new file mode 100644
index 0000000..5ebd6ff
--- /dev/null
+++ b/src/jaligner/ui/filechooser/FileChooserTrusted.java
@@ -0,0 +1,104 @@
+/*
+ * $Id: FileChooserTrusted.java,v 1.12 2005/01/10 15:01:01 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.filechooser;
+
+
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.util.logging.Logger;
+
+import javax.swing.JFileChooser;
+
+/**
+ * Opens and saves files.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class FileChooserTrusted extends FileChooser {
+ private static final Logger logger = Logger.getLogger(FileChooserJNLP.class.getName());
+
+ /**
+ * Shows a dialog to select a file.
+ * @return input stream
+ * @throws FileChooserException
+ * @see NamedInputStream
+ */
+ public NamedInputStream open() throws FileChooserException {
+ try {
+ JFileChooser chooser = new JFileChooser( );
+ chooser.setCurrentDirectory(new File(getUserDirectory()));
+ int returnVal = chooser.showOpenDialog(null);
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ setUserDirectory(chooser.getCurrentDirectory().toString());
+ logger.info("Loaded: " + chooser.getSelectedFile().getName());
+ return new NamedInputStream(chooser.getSelectedFile().getName(),
+ new FileInputStream(chooser.getSelectedFile()));
+ } else {
+ return null;
+ }
+ } catch (Exception e) {
+ String message = "Failed open: " + e.getMessage();
+ logger.warning(message);
+ throw new FileChooserException(message);
+ }
+ }
+
+ /**
+ * Saves an input stream to a file.
+ *
+ * @param is
+ * @param fileName
+ * @return boolean
+ * @throws FileChooserException
+ */
+ public boolean save(InputStream is, String fileName) throws FileChooserException {
+ try {
+ JFileChooser chooser = new JFileChooser( );
+ chooser.setCurrentDirectory(new File(getUserDirectory()));
+ if (fileName != null) {
+ chooser.setSelectedFile(new File(fileName));
+ }
+ int returnVal = chooser.showSaveDialog(null);
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ setUserDirectory(chooser.getCurrentDirectory().toString());
+ File file = chooser.getSelectedFile();
+ logger.info("Saved: " + file.getName());
+ FileOutputStream fos = new FileOutputStream(file);
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int len;
+ while ((len = is.read(buffer)) != -1) {
+ fos.write(buffer, 0, len);
+ }
+ fos.close();
+ is.close();
+ return true;
+ } else {
+ return false;
+ }
+ } catch (Exception e) {
+ String message = "Failed save: " + e.getMessage();
+ logger.warning(message);
+ throw new FileChooserException(message);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/NamedInputStream.java b/src/jaligner/ui/filechooser/NamedInputStream.java
new file mode 100644
index 0000000..6ee46ac
--- /dev/null
+++ b/src/jaligner/ui/filechooser/NamedInputStream.java
@@ -0,0 +1,67 @@
+/*
+ * $Id: NamedInputStream.java,v 1.2 2005/04/14 14:44:43 ahmed Exp $
+ *
+ * This program inputStream free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program inputStream distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.filechooser;
+
+import java.io.InputStream;
+import java.io.Serializable;
+
+/**
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class NamedInputStream extends Object implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3256441404384686387L;
+
+ /**
+ * Name.
+ */
+ private String name = null;
+
+ /**
+ * Input stream.
+ */
+ private InputStream inputStream = null;
+
+ /**
+ *
+ */
+ public NamedInputStream(String name, InputStream inputStream) {
+ this.name = name;
+ this.inputStream = inputStream;
+ }
+
+ /**
+ * @return Returns the inputStream.
+ */
+ public InputStream getInputStream() {
+ return this.inputStream;
+ }
+
+ /**
+ * @return Returns the name.
+ */
+ public String getName() {
+ return this.name;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/package.html b/src/jaligner/ui/filechooser/package.html
new file mode 100644
index 0000000..437cb06
--- /dev/null
+++ b/src/jaligner/ui/filechooser/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.2 2005/04/05 13:43:32 ahmed Exp $--></head>
+<body bgcolor="white">
+File loading and storing.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/images/ToolbarIcons.java b/src/jaligner/ui/images/ToolbarIcons.java
new file mode 100644
index 0000000..4864d27
--- /dev/null
+++ b/src/jaligner/ui/images/ToolbarIcons.java
@@ -0,0 +1,79 @@
+/*
+ * $Id: ToolbarIcons.java,v 1.3 2005/02/17 07:14:56 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.images;
+
+import javax.swing.ImageIcon;
+
+/**
+ * Toolbar icons
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public abstract class ToolbarIcons {
+ /**
+ * Path to the gifs folder
+ */
+ public static final String GIFS_HOME = "/jaligner/ui/images/gifs/";
+
+ /**
+ * Open icon
+ */
+ public static final ImageIcon OPEN = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "open.gif"));
+
+ /**
+ * Save icon
+ */
+ public static final ImageIcon SAVE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "save.gif"));
+
+ /**
+ * Cut icon
+ */
+ public static final ImageIcon CUT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "cut.gif"));
+
+ /**
+ * Copy icon
+ */
+ public static final ImageIcon COPY = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "copy.gif"));
+
+ /**
+ * Paste icon
+ */
+ public static final ImageIcon PASTE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "paste.gif"));
+
+ /**
+ * Delete icon
+ */
+ public static final ImageIcon DELETE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "delete.gif"));
+
+ /**
+ * Close icon
+ */
+ public static final ImageIcon CLOSE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "close.gif"));
+
+ /**
+ * About icon
+ */
+ public static final ImageIcon ABOUT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "about.gif"));
+
+
+ /**
+ * Print icon
+ */
+ public static final ImageIcon PRINT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "print.gif"));
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/images/gifs/about.gif b/src/jaligner/ui/images/gifs/about.gif
new file mode 100644
index 0000000..04da95e
Binary files /dev/null and b/src/jaligner/ui/images/gifs/about.gif differ
diff --git a/src/jaligner/ui/images/gifs/close.gif b/src/jaligner/ui/images/gifs/close.gif
new file mode 100644
index 0000000..064202b
Binary files /dev/null and b/src/jaligner/ui/images/gifs/close.gif differ
diff --git a/src/jaligner/ui/images/gifs/copy.gif b/src/jaligner/ui/images/gifs/copy.gif
new file mode 100644
index 0000000..fa98681
Binary files /dev/null and b/src/jaligner/ui/images/gifs/copy.gif differ
diff --git a/src/jaligner/ui/images/gifs/cut.gif b/src/jaligner/ui/images/gifs/cut.gif
new file mode 100644
index 0000000..14b73a8
Binary files /dev/null and b/src/jaligner/ui/images/gifs/cut.gif differ
diff --git a/src/jaligner/ui/images/gifs/delete.gif b/src/jaligner/ui/images/gifs/delete.gif
new file mode 100644
index 0000000..d9d1a33
Binary files /dev/null and b/src/jaligner/ui/images/gifs/delete.gif differ
diff --git a/src/jaligner/ui/images/gifs/jaligner.gif b/src/jaligner/ui/images/gifs/jaligner.gif
new file mode 100644
index 0000000..4711572
Binary files /dev/null and b/src/jaligner/ui/images/gifs/jaligner.gif differ
diff --git a/src/jaligner/ui/images/gifs/open.gif b/src/jaligner/ui/images/gifs/open.gif
new file mode 100644
index 0000000..fabd567
Binary files /dev/null and b/src/jaligner/ui/images/gifs/open.gif differ
diff --git a/src/jaligner/ui/images/gifs/paste.gif b/src/jaligner/ui/images/gifs/paste.gif
new file mode 100644
index 0000000..f118c7e
Binary files /dev/null and b/src/jaligner/ui/images/gifs/paste.gif differ
diff --git a/src/jaligner/ui/images/gifs/print.gif b/src/jaligner/ui/images/gifs/print.gif
new file mode 100644
index 0000000..7eb8299
Binary files /dev/null and b/src/jaligner/ui/images/gifs/print.gif differ
diff --git a/src/jaligner/ui/images/gifs/save.gif b/src/jaligner/ui/images/gifs/save.gif
new file mode 100644
index 0000000..8d3929c
Binary files /dev/null and b/src/jaligner/ui/images/gifs/save.gif differ
diff --git a/src/jaligner/ui/images/package.html b/src/jaligner/ui/images/package.html
new file mode 100644
index 0000000..5c792c9
--- /dev/null
+++ b/src/jaligner/ui/images/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.1 2005/04/05 02:18:52 ahmed Exp $--></head>
+<body bgcolor="white">
+Images used in the toolbar.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/logging/DocumentHandler.java b/src/jaligner/ui/logging/DocumentHandler.java
new file mode 100644
index 0000000..b96c775
--- /dev/null
+++ b/src/jaligner/ui/logging/DocumentHandler.java
@@ -0,0 +1,118 @@
+/*
+ * $Id: DocumentHandler.java,v 1.6 2005/02/22 06:11:58 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.logging;
+
+import java.awt.Color;
+import java.util.logging.ErrorManager;
+import java.util.logging.Handler;
+import java.util.logging.Level;
+import java.util.logging.LogRecord;
+
+import javax.swing.JTextPane;
+import javax.swing.text.Style;
+import javax.swing.text.StyleConstants;
+import javax.swing.text.StyledDocument;
+
+/**
+ * Logging handler of {@link javax.swing.JTextPane}.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class DocumentHandler extends Handler {
+ /**
+ * Maximum document size
+ */
+ private static final int MAXIMUM_DOCUMENT_SIZE = 524288; // 0.5 MB
+
+ private JTextPane textPane = null;
+ private Style infoStyle = null;
+ private Style severStyle = null;
+
+ /**
+ * Constructor
+ * @param textPane
+ */
+ public DocumentHandler(JTextPane textPane) {
+ this.textPane = textPane;
+ setFormatter(new RecordFormatter());
+
+ StyledDocument document = (StyledDocument) this.textPane.getDocument();
+
+ infoStyle = document.addStyle("INFO", null);
+ StyleConstants.setFontFamily(infoStyle,"Monospaced");
+ StyleConstants.setBackground(infoStyle, Color.white);
+ StyleConstants.setForeground(infoStyle, Color.blue);
+
+ severStyle = document.addStyle("SEVER", null);
+ StyleConstants.setFontFamily(severStyle,"Monospaced");
+ StyleConstants.setBackground(severStyle, Color.white);
+ StyleConstants.setForeground(severStyle, Color.red);
+ }
+
+
+ /**
+ *
+ */
+ public void close() {
+ }
+
+ /**
+ *
+ */
+ public void flush() {
+ }
+
+ /**
+ *
+ */
+ public void publish(LogRecord record) {
+ if (!isLoggable(record)) {
+ return;
+ }
+
+ String message;
+
+ try {
+ message = getFormatter().format(record);
+ } catch (Exception exception) {
+ reportError(null, exception, ErrorManager.FORMAT_FAILURE);
+ return;
+ }
+
+ synchronized(textPane) {
+ if (textPane.getDocument().getLength() >= MAXIMUM_DOCUMENT_SIZE) {
+ // Delete the contents of the text pane.
+ textPane.setText("");
+ }
+
+ try {
+ if (record.getLevel() == Level.SEVERE) {
+ textPane.getDocument().insertString(textPane.getDocument().getLength(), message, severStyle);
+ } else {
+ textPane.getDocument().insertString(textPane.getDocument().getLength(), message, infoStyle);
+ }
+ textPane.setCaretPosition(textPane.getDocument().getLength());
+ } catch (Exception ex) {
+ reportError(null, ex, ErrorManager.WRITE_FAILURE);
+ }
+ }
+
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/logging/RecordFormatter.java b/src/jaligner/ui/logging/RecordFormatter.java
new file mode 100644
index 0000000..bae1955
--- /dev/null
+++ b/src/jaligner/ui/logging/RecordFormatter.java
@@ -0,0 +1,70 @@
+/*
+ * $Id: RecordFormatter.java,v 1.6 2005/02/19 14:58:10 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.logging;
+
+import java.util.Date;
+import java.util.logging.Formatter;
+import java.util.logging.Handler;
+import java.util.logging.LogRecord;
+
+/**
+ * Logging record formatter
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class RecordFormatter extends Formatter {
+
+ /**
+ * This method is called for every log records
+ *
+ * @param record
+ */
+ public String format(LogRecord record) {
+ StringBuffer buffer = new StringBuffer( );
+ buffer.append ( new Date().toString() );
+ buffer.append ( " " );
+ buffer.append ( record.getLevel() );
+ buffer.append ( "\t" );
+ buffer.append ( record.getMessage() );
+ buffer.append ( "\n" );
+
+ return buffer.toString();
+ }
+
+ /**
+ * This method is called just after the handler using this
+ * formatter is created
+ *
+ * @param handler
+ */
+ public String getHead(Handler handler) {
+ return "";
+ }
+
+ /**
+ * This method is called just after the handler using this
+ * formatter is closed
+ *
+ * @param handler
+ */
+ public String getTail(Handler handler) {
+ return "\n";
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/logging/package.html b/src/jaligner/ui/logging/package.html
new file mode 100644
index 0000000..4506adc
--- /dev/null
+++ b/src/jaligner/ui/logging/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.3 2005/04/05 13:43:32 ahmed Exp $--></head>
+<body bgcolor="white">
+Logging package.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/package.html b/src/jaligner/ui/package.html
new file mode 100644
index 0000000..cf56259
--- /dev/null
+++ b/src/jaligner/ui/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.5 2005/04/05 13:43:32 ahmed Exp $--></head>
+<body bgcolor="white">
+Command line and graphical user interface.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/util/PrintJobMointor.java b/src/jaligner/ui/util/PrintJobMointor.java
new file mode 100644
index 0000000..8329caa
--- /dev/null
+++ b/src/jaligner/ui/util/PrintJobMointor.java
@@ -0,0 +1,89 @@
+/*
+ * $Id: PrintJobMointor.java,v 1.2 2005/02/19 14:58:10 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.util;
+
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.print.DocPrintJob;
+import javax.print.event.PrintJobAdapter;
+import javax.print.event.PrintJobEvent;
+
+/**
+ * Mointor for print job.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class PrintJobMointor {
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger.getLogger(TextComponentUtil.class.getName());
+
+ // True iff it is safe to close the print job's input stream
+ private boolean done = false;
+
+ PrintJobMointor(DocPrintJob job) {
+ // Add a listener to the print job
+ job.addPrintJobListener(new PrintJobAdapter() {
+ public void printJobCanceled(PrintJobEvent printJobEvent) {
+ logger.info("Print job canceled");
+ allDone();
+ }
+
+ public void printJobCompleted(PrintJobEvent printJobEvent) {
+ logger.info("Print job completed");
+ allDone();
+ }
+
+ public void printJobFailed(PrintJobEvent printJobEvent) {
+ logger.info("Print job failed");
+ allDone();
+ }
+
+ public void printJobNoMoreEvents(PrintJobEvent printJobEvent) {
+ allDone();
+ }
+
+ void allDone() {
+ synchronized (PrintJobMointor.this) {
+ done = true;
+ PrintJobMointor.this.notify();
+ }
+ }
+ });
+ }
+
+ /**
+ * Waits for print job
+ *
+ */
+ public synchronized void waitForPrintJob() {
+ try {
+ logger.info("Waiting for print job...");
+ while (!done) {
+ wait();
+ }
+ logger.info("Finished waiting for print");
+ } catch (InterruptedException e) {
+ logger.log(Level.SEVERE, "Failed waiting for print job: " + e.getMessage(), e);
+ }
+ }
+}
diff --git a/src/jaligner/ui/util/TextComponentUtil.java b/src/jaligner/ui/util/TextComponentUtil.java
new file mode 100644
index 0000000..954f64b
--- /dev/null
+++ b/src/jaligner/ui/util/TextComponentUtil.java
@@ -0,0 +1,281 @@
+/*
+ * $Id: TextComponentUtil.java,v 1.14 2005/04/15 15:03:15 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.util;
+
+import jaligner.ui.clipboard.ClipboardHandlerFactory;
+import jaligner.ui.filechooser.FileChooserFactory;
+import jaligner.ui.filechooser.NamedInputStream;
+import jaligner.util.Commons;
+
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.print.Doc;
+import javax.print.DocFlavor;
+import javax.print.DocPrintJob;
+import javax.print.PrintService;
+import javax.print.PrintServiceLookup;
+import javax.print.ServiceUI;
+import javax.print.SimpleDoc;
+import javax.print.attribute.HashDocAttributeSet;
+import javax.print.attribute.HashPrintRequestAttributeSet;
+import javax.print.attribute.PrintRequestAttributeSet;
+import javax.print.attribute.standard.DocumentName;
+import javax.print.attribute.standard.JobName;
+import javax.swing.text.Document;
+import javax.swing.text.JTextComponent;
+
+/**
+ * Text component (e.g. {@link javax.swing.JTextArea}or
+ * {@link javax.swing.JTextPane}) editing helper class.
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class TextComponentUtil {
+ /**
+ * Empty string
+ */
+ private static final String EMPTY = "";
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger
+ .getLogger(TextComponentUtil.class.getName());
+
+ /**
+ * Copies the selected text to the system clipboad and then deletes it from
+ * the text component.
+ *
+ * @param textComponent
+ */
+ public static void cut(JTextComponent textComponent) {
+ copy(textComponent);
+ delete(textComponent);
+ }
+
+ /**
+ * Copies the selected text to the system clipboard.
+ *
+ * @param textComponent
+ */
+ public static void copy(JTextComponent textComponent) {
+ ClipboardHandlerFactory.getClipboardHandler().setContents(
+ textComponent.getSelectedText());
+ }
+
+ /**
+ * Copies the text contents of the system clipboard to the text component.
+ *
+ * @param textComponent
+ */
+ public static void paste(JTextComponent textComponent) {
+ String contents = ClipboardHandlerFactory.getClipboardHandler()
+ .getContents();
+ if (contents != null) {
+ StringBuffer buffer = new StringBuffer();
+ char c;
+ for (int i = 0, n = contents.length(); i < n; i++) {
+ c = contents.charAt(i);
+ // Not to copy a null character
+ if (c != 0) {
+ buffer.append(c);
+ }
+ }
+ textComponent.replaceSelection(buffer.toString());
+ }
+ if (!textComponent.hasFocus()) {
+ textComponent.requestFocus();
+ }
+ }
+
+ /**
+ * Deletes the selected text in a text component.
+ *
+ * @param textComponent
+ */
+ public static void delete(JTextComponent textComponent) {
+ textComponent.replaceSelection(EMPTY);
+ }
+
+ /**
+ * Selects all contents of a text component.
+ *
+ * @param textComponent
+ */
+ public static void selectAll(JTextComponent textComponent) {
+ if (!textComponent.hasFocus()) {
+ textComponent.requestFocus();
+ }
+ textComponent.selectAll();
+ }
+
+ /**
+ * Opens a file and puts the contents of the file in a text component.
+ *
+ * @param textComponent
+ * @throws TextComponentUtilException
+ */
+ public static boolean open(JTextComponent textComponent)
+ throws TextComponentUtilException {
+ InputStream is = null;
+ BufferedReader reader = null;
+ try {
+ NamedInputStream selectedInputStream = FileChooserFactory
+ .getFileChooser().open();
+ if (selectedInputStream != null) {
+ is = selectedInputStream.getInputStream();
+ textComponent.setText(EMPTY);
+
+ reader = new BufferedReader(new InputStreamReader(is));
+ String line;
+ Document document = textComponent.getDocument();
+ while ((line = reader.readLine()) != null) {
+ document.insertString(document.getLength(), line
+ + Commons.getLineSeparator(), null);
+ }
+ if (!textComponent.hasFocus()) {
+ textComponent.requestFocus();
+ }
+ return true;
+ } else {
+ return false;
+ }
+ } catch (Exception e) {
+ throw new TextComponentUtilException(e.getMessage());
+ } finally {
+ if (is != null) {
+ try {
+ is.close();
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed closing input stream: "
+ + e.getMessage(), e);
+ }
+ }
+ if (reader != null) {
+ try {
+ reader.close();
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed closing reader: "
+ + e.getMessage(), e);
+ }
+ }
+ }
+ }
+
+ /**
+ * Saves the contents of a text component to a file.
+ *
+ * @param textComponent
+ * @param fileName
+ * @return true if a file has been chosen or false otherwise
+ * @throws TextComponentUtilException
+ */
+ public static boolean save(JTextComponent textComponent, String fileName)
+ throws TextComponentUtilException {
+ InputStream is = null;
+ try {
+ is = new ByteArrayInputStream(textComponent.getText().getBytes());
+ return FileChooserFactory.getFileChooser().save(is, fileName);
+ } catch (Exception e) {
+ throw new TextComponentUtilException(e.getMessage());
+ } finally {
+ try {
+ is.close();
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed closing input stream: "
+ + e.getMessage(), e);
+ }
+ }
+ }
+
+ /**
+ * Saves the contents of a text component to a file.
+ *
+ * @param textComponent
+ * @return true if a file has been chosen or false otherwise
+ * @throws TextComponentUtilException
+ */
+ public static boolean save(JTextComponent textComponent)
+ throws TextComponentUtilException {
+ return save(textComponent, null);
+ }
+
+ /**
+ * Prints the contents of a text component.
+ *
+ * @param textComponent
+ */
+ public static void print(JTextComponent textComponent)
+ throws TextComponentUtilException {
+ InputStream is = null;
+ try {
+ PrintService[] printServices = PrintServiceLookup
+ .lookupPrintServices(DocFlavor.INPUT_STREAM.AUTOSENSE, null);
+ if (printServices.length > 0) {
+
+ PrintRequestAttributeSet printRequestAttributeSet = new HashPrintRequestAttributeSet();
+ printRequestAttributeSet.add(new JobName("JAligner", null));
+ PrintService service = ServiceUI.printDialog(null, 50, 50,
+ printServices, PrintServiceLookup
+ .lookupDefaultPrintService(),
+ DocFlavor.INPUT_STREAM.AUTOSENSE,
+ printRequestAttributeSet);
+
+ if (service != null) {
+ DocPrintJob printJob = service.createPrintJob();
+ PrintJobMointor printJobMointor = new PrintJobMointor(
+ printJob);
+
+ is = new ByteArrayInputStream(textComponent.getText()
+ .getBytes());
+
+ DocumentName documentName = new DocumentName("JAligner",
+ null);
+ HashDocAttributeSet docAttributeSet = new HashDocAttributeSet();
+ docAttributeSet.add(documentName);
+ Doc doc = new SimpleDoc(is,
+ DocFlavor.INPUT_STREAM.AUTOSENSE, docAttributeSet);
+
+ printJob.print(doc, printRequestAttributeSet);
+ printJobMointor.waitForPrintJob();
+ }
+ } else {
+ throw new TextComponentUtilException("No print service found!");
+ }
+ } catch (Exception e) {
+ throw new TextComponentUtilException(e.getMessage());
+ } finally {
+ if (is != null) {
+ try {
+ is.close();
+ } catch (IOException e) {
+ logger.log(Level.WARNING, "Failed closing input stream: "
+ + e.getMessage(), e);
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/ui/util/TextComponentUtilException.java b/src/jaligner/ui/util/TextComponentUtilException.java
new file mode 100644
index 0000000..d99df09
--- /dev/null
+++ b/src/jaligner/ui/util/TextComponentUtilException.java
@@ -0,0 +1,39 @@
+/*
+ * $Id: TextComponentUtilException.java,v 1.2 2005/04/14 14:44:44 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.ui.util;
+
+/**
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class TextComponentUtilException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 4050763797251567922L;
+
+ /**
+ * @param message
+ */
+ public TextComponentUtilException(String message) {
+ super(message);
+ }
+}
diff --git a/src/jaligner/ui/util/package.html b/src/jaligner/ui/util/package.html
new file mode 100644
index 0000000..a98316d
--- /dev/null
+++ b/src/jaligner/ui/util/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.6 2005/02/19 12:54:38 ahmed Exp $--></head>
+<body bgcolor="white">
+Text component utilites package.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
diff --git a/src/jaligner/util/Commons.java b/src/jaligner/util/Commons.java
new file mode 100644
index 0000000..8bf93c3
--- /dev/null
+++ b/src/jaligner/util/Commons.java
@@ -0,0 +1,217 @@
+/*
+ * $Id: Commons.java,v 1.27 2005/04/18 05:37:52 ahmed Exp $
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.util;
+
+import java.net.JarURLConnection;
+import java.net.URL;
+import java.util.jar.Attributes;
+import java.util.jar.JarFile;
+import java.util.jar.Manifest;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Global constants/varilables/settings
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public abstract class Commons {
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger.getLogger(Commons.class
+ .getName());
+
+ /**
+ * Build timestamp attribute in the manifest in the jar
+ */
+ private static final String BUILD_TIMESTAMP = "Created-At";
+
+ /**
+ *
+ */
+ private static final String currentRelease = getManifestBuildTimestamp();
+
+ /**
+ * Default home directory
+ */
+ private static final String DEFAULT_USER_DIRECTORY = ".";
+
+ /**
+ * Default file separator
+ */
+ private static final String DEFAULT_FILE_SEPARATOR = "/";
+
+ /**
+ * Default line separator
+ */
+ private static final String DEFAULT_LINE_SEPARATOR = "\r\n";
+
+ /**
+ * User home directory
+ */
+ private static String userDirectory = DEFAULT_USER_DIRECTORY;
+ static {
+ try {
+ userDirectory = System.getProperty("user.dir");
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting user current directory: "
+ + e.getMessage(), e);
+ }
+ }
+
+ /**
+ * Line separator
+ */
+ private static String fileSeparator = DEFAULT_FILE_SEPARATOR;
+ static {
+ try {
+ fileSeparator = System.getProperty("file.separator");
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting system file separator: "
+ + e.getMessage(), e);
+ }
+ }
+
+ /**
+ * Line separator
+ */
+ private static String lineSeparator = DEFAULT_LINE_SEPARATOR;
+
+ static {
+ try {
+ lineSeparator = System.getProperty("line.separator");
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting system line separator: "
+ + e.getMessage(), e);
+ }
+ }
+
+ /**
+ * JNLP enabled
+ */
+ private static boolean jnlp = false;
+ static {
+ try {
+ jnlp = "true".equalsIgnoreCase(System.getProperty("jnlp.enabled"));
+ } catch (Exception e) {
+ logger.log(Level.WARNING, "Failed getting jnlp enabled property: "
+ + e.getMessage(), e);
+ }
+ setJnlp(jnlp);
+ }
+
+ /**
+ * Returns system file separator.
+ *
+ * @return file separator
+ */
+ public static String getFileSeparator() {
+ return fileSeparator;
+ }
+
+ /**
+ * Returns system line separator.
+ *
+ * @return line separator
+ */
+ public static String getLineSeparator() {
+ return lineSeparator;
+ }
+
+ /**
+ * Returns user's current directory.
+ *
+ * @return user's current directory
+ */
+ public static String getUserDirectory() {
+ return userDirectory;
+ }
+
+ /**
+ * Sets the JNLP flag to true of false
+ *
+ * @param jnlp
+ * true or false
+ */
+ public static void setJnlp(boolean jnlp) {
+ Commons.jnlp = jnlp;
+ }
+
+ /**
+ * Returns true if jnlp is enabled
+ *
+ * @return true if jnlp is enabled, otherwise returns false
+ */
+ public static boolean isJnlp() {
+ return jnlp;
+ }
+
+ /**
+ * Gets the build teimstamp from the jar manifest
+ *
+ * @return build timestamp
+ */
+ private static String getManifestBuildTimestamp() {
+ JarURLConnection connection = null;
+ JarFile jarFile = null;
+ URL url = Commons.class.getClassLoader().getResource("jaligner");
+ try {
+ // Get jar connection
+ connection = (JarURLConnection) url.openConnection();
+
+ // Get the jar file
+ jarFile = connection.getJarFile();
+
+ // Get the manifest
+ Manifest manifest = jarFile.getManifest();
+
+ // Get the manifest entries
+ Attributes attributes = manifest.getMainAttributes();
+
+ Attributes.Name name = new Attributes.Name(BUILD_TIMESTAMP);
+ return attributes.getValue(name);
+ } catch (Exception e) {
+ String message = "Failed getting the current release info: "
+ + e.getMessage();
+ logger.log(Level.WARNING, message);
+ }
+ return null;
+ }
+
+ /**
+ * Returns the current release version of JAligner
+ *
+ * @return current release
+ */
+ public static String getCurrentRelease() {
+ return currentRelease;
+ }
+
+ /**
+ * Returns information about JAligner
+ *
+ * @return information about JAligner
+ */
+ public static String getJAlignerInfo() {
+ return "JAligner - Build: " + getCurrentRelease()
+ + " - By: Ahmed Moustafa (ahmed at users.sf.net)";
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/util/SequenceParser.java b/src/jaligner/util/SequenceParser.java
new file mode 100644
index 0000000..27ee681
--- /dev/null
+++ b/src/jaligner/util/SequenceParser.java
@@ -0,0 +1,215 @@
+/*
+ * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.util;
+
+
+import jaligner.Sequence;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+import java.util.StringTokenizer;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * SequenceParser to sequences from different formats.
+ * <br>
+ * Currently the supported formats are:
+ * <ul>
+ * <li>Plain sequence</li>
+ * <li><a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">Sequence</a></li>
+ * </ul>
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class SequenceParser {
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger.getLogger(SequenceParser.class.getName());
+
+ /**
+ * Returns a parsed Sequence from a string.
+ * @param sequence string to parse
+ * @return parsed sequence
+ * @throws SequenceParserException
+ * @see Sequence
+ */
+ public static Sequence parse (String sequence) throws SequenceParserException {
+ if (sequence == null) {
+ throw new SequenceParserException ( "Null sequence" );
+ }
+
+ if (sequence.trim().length() == 0) {
+ throw new SequenceParserException ( "Empty sequence" );
+ }
+
+ sequence = sequence.replaceAll("\r\n", "\n");
+
+ String sequenceName = null;
+ String sequenceDescription = null;
+
+ if (sequence.startsWith(">")) {
+ // FASTA format
+ int index = sequence.indexOf("\n");
+
+ if (index == -1) {
+ throw new SequenceParserException ( "Invalid sequence format" );
+ }
+
+ String first = sequence.substring(1, index);
+ sequence = sequence.substring(index);
+
+ index = 0;
+ for (int i = 0; i < first.length() && first.charAt(i) != ' ' && first.charAt(i) != '\t'; i++, index++) {
+ // Skip white spaces
+ }
+ sequenceName = first.substring(0, index);
+ StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|");
+ while (stringTokenizer.hasMoreTokens()) {
+ sequenceName = stringTokenizer.nextToken();
+ }
+ sequenceDescription = index + 1 > first.length() ? "" : first.substring(index + 1);
+ } else {
+ // Plain format ... nothing to do here
+ }
+
+ Sequence s = new Sequence(prepare(sequence), sequenceName, sequenceDescription, Sequence.PROTEIN);
+
+ return s;
+ }
+
+ /**
+ * Returns a Sequence parsed and loaded from a file
+ * @param file to parse
+ * @return parsed sequence
+ * @throws SequenceParserException
+ * @see Sequence
+ */
+ public static Sequence parse (File file) throws SequenceParserException {
+ String sequenceName = null;
+ String sequenceDescription = null;
+ BufferedReader reader = null;
+ try {
+ reader = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
+ StringBuffer buffer = new StringBuffer();
+
+ // Read & parse the first line
+ String line = reader.readLine();
+
+ if (line.startsWith(">")) {
+ // FASTA sequence
+
+ line = line.substring(1).trim();
+ int index = 0;
+ for (int i = 0; i < line.length() && line.charAt(i) != ' ' && line.charAt(i) != '\t'; i++, index++) {
+ // Skip white spaces
+ }
+
+ sequenceName = line.substring(0, index);
+ StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|");
+ while (stringTokenizer.hasMoreTokens()) {
+ sequenceName = stringTokenizer.nextToken();
+ }
+ sequenceDescription = index + 1 > line.length() ? "" : line.substring(index + 1);
+ } else {
+ // Plain sequence
+ buffer.append(prepare(line));
+ }
+
+ // Read the remaining the file (the actual sequence)
+ while ((line = reader.readLine()) != null) {
+ buffer.append(prepare(line));
+ }
+ reader.close();
+
+ Sequence s = new Sequence(buffer.toString(), sequenceName, sequenceDescription, Sequence.PROTEIN);
+ return s;
+ } catch (Exception e) {
+ throw new SequenceParserException(e.getMessage());
+ } finally {
+ if (reader != null) {
+ try {
+ reader.close();
+ } catch (Exception silent) {
+ logger.log(Level.WARNING, "Failed closing reader: " + silent.getMessage(), silent);
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Removes whitespaces from a sequence and validates other characters.
+ * @param sequence sequence to be prepared
+ * @return prepared array of characters
+ * @throws SequenceParserException
+ */
+ private static String prepare (String sequence) throws SequenceParserException {
+ StringBuffer buffer = new StringBuffer();
+ String copy = sequence.trim().toUpperCase();
+
+ for (int i = 0, n = copy.length(); i < n; i++) {
+ switch ( copy.charAt(i) ) {
+ // skip whitespaces
+ case 9:
+ case 10:
+ case 13:
+ case 32: break;
+
+ // add a valid character
+ case 'A':
+ case 'B':
+ case 'C':
+ case 'D':
+ case 'E':
+ case 'F':
+ case 'G':
+ case 'H':
+ case 'I':
+ case 'K':
+ case 'L':
+ case 'M':
+ case 'N':
+ case 'P':
+ case 'Q':
+ case 'R':
+ case 'S':
+ case 'T':
+ case 'U':
+ case 'V':
+ case 'W':
+ case 'Y':
+ case 'Z':
+ case 'X':
+
+ case '-':
+ case '*': buffer.append(copy.charAt(i)); break;
+
+ // throw an exception for anything else
+ default: throw new SequenceParserException( "Invalid sequence character: '" + copy.charAt(i) + "'");
+ }
+ }
+ return buffer.toString();
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/util/SequenceParserException.java b/src/jaligner/util/SequenceParserException.java
new file mode 100644
index 0000000..450169f
--- /dev/null
+++ b/src/jaligner/util/SequenceParserException.java
@@ -0,0 +1,38 @@
+/*
+ * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jaligner.util;
+
+/**
+ *
+ * @author Ahmed Moustafa (ahmed at users.sf.net)
+ */
+
+public class SequenceParserException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3258417248288191543L;
+
+ /**
+ * @param message
+ */
+ public SequenceParserException(String message) {
+ super(message);
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/util/package.html b/src/jaligner/util/package.html
new file mode 100644
index 0000000..9223585
--- /dev/null
+++ b/src/jaligner/util/package.html
@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head><!--$Id: package.html,v 1.7 2005/04/05 13:43:32 ahmed Exp $--></head>
+<body bgcolor="white">
+Utility classes for helping core and GUI classes.
+ at author Ahmed Moustafa (ahmed at users.sf.net)
+</body>
+</html>
\ No newline at end of file
--
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