[med-svn] [jaligner] 01/04: Imported Upstream version 1.0
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 06:35:35 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository jaligner.
commit 2b5d5aa9313cf4001c2e0c5b67629c63433230f9
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 01:22:58 2015 -0500
Imported Upstream version 1.0
---
README | 4 +-
README.md | 2 +
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 57 -> 0 bytes
api/serialized-form.html | 1232 --------------------
build.properties | 16 +-
build.xml | 111 +-
jaligner.bat | 1 -
jaligner.css | 38 -
jaligner.jar | Bin 164489 -> 182588 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 | 292 ++++-
src/jaligner/Cell.java | 4 +-
src/jaligner/Directions.java | 4 +-
src/jaligner/Markups.java | 4 +-
src/jaligner/NeedlemanWunsch.java | 302 +++++
src/jaligner/NeedlemanWunschGotoh.java | 427 +++++++
src/jaligner/Sequence.java | 272 +++--
src/jaligner/SmithWatermanGotoh.java | 79 +-
src/jaligner/TracebackNode.java | 97 ++
src/jaligner/example/NeedlemanWunschExample.java | 72 ++
.../example/NeedlemanWunschGotohExample.java | 91 ++
...Example.java => SmithWatermanGotohExample.java} | 10 +-
src/jaligner/example/package.html | 4 +-
src/jaligner/example/sequences/p53_human.fasta | 12 +-
src/jaligner/example/sequences/p53_mouse.fasta | 14 +-
src/jaligner/formats/CLUSTAL.java | 4 +-
src/jaligner/formats/FASTA.java | 4 +-
src/jaligner/formats/Format.java | 4 +-
src/jaligner/formats/FormatFactory.java | 8 +-
src/jaligner/formats/Pair.java | 6 +-
src/jaligner/formats/package.html | 4 +-
src/jaligner/matrix/MatricesCompartor.java | 11 +-
src/jaligner/matrix/Matrix.java | 95 +-
src/jaligner/matrix/MatrixGenerator.java | 59 +
src/jaligner/matrix/MatrixLoader.java | 170 +--
src/jaligner/matrix/MatrixLoaderException.java | 4 +-
src/jaligner/matrix/matrices/BLOSUM100 | 62 +-
src/jaligner/matrix/matrices/BLOSUM30 | 62 +-
src/jaligner/matrix/matrices/BLOSUM35 | 62 +-
src/jaligner/matrix/matrices/BLOSUM40 | 62 +-
src/jaligner/matrix/matrices/BLOSUM45 | 62 +-
src/jaligner/matrix/matrices/BLOSUM50 | 62 +-
src/jaligner/matrix/matrices/BLOSUM55 | 62 +-
src/jaligner/matrix/matrices/BLOSUM60 | 62 +-
src/jaligner/matrix/matrices/BLOSUM62 | 62 +-
src/jaligner/matrix/matrices/BLOSUM65 | 62 +-
src/jaligner/matrix/matrices/BLOSUM70 | 62 +-
src/jaligner/matrix/matrices/BLOSUM75 | 62 +-
src/jaligner/matrix/matrices/BLOSUM80 | 62 +-
src/jaligner/matrix/matrices/BLOSUM85 | 62 +-
src/jaligner/matrix/matrices/BLOSUM90 | 62 +-
src/jaligner/matrix/matrices/BLOSUMN | 62 +-
src/jaligner/matrix/matrices/DAYHOFF | 64 +-
src/jaligner/matrix/matrices/EDNAFULL | 50 +-
src/jaligner/matrix/matrices/GONNET | 52 +-
src/jaligner/matrix/matrices/IDENTITY | 50 +-
src/jaligner/matrix/matrices/MATCH | 50 +-
src/jaligner/matrix/matrices/PAM10 | 68 +-
src/jaligner/matrix/matrices/PAM100 | 68 +-
src/jaligner/matrix/matrices/PAM110 | 68 +-
src/jaligner/matrix/matrices/PAM120 | 68 +-
src/jaligner/matrix/matrices/PAM130 | 68 +-
src/jaligner/matrix/matrices/PAM140 | 68 +-
src/jaligner/matrix/matrices/PAM150 | 68 +-
src/jaligner/matrix/matrices/PAM160 | 68 +-
src/jaligner/matrix/matrices/PAM170 | 68 +-
src/jaligner/matrix/matrices/PAM180 | 68 +-
src/jaligner/matrix/matrices/PAM190 | 68 +-
src/jaligner/matrix/matrices/PAM20 | 68 +-
src/jaligner/matrix/matrices/PAM200 | 68 +-
src/jaligner/matrix/matrices/PAM210 | 68 +-
src/jaligner/matrix/matrices/PAM220 | 68 +-
src/jaligner/matrix/matrices/PAM230 | 68 +-
src/jaligner/matrix/matrices/PAM240 | 68 +-
src/jaligner/matrix/matrices/PAM250 | 68 +-
src/jaligner/matrix/matrices/PAM260 | 68 +-
src/jaligner/matrix/matrices/PAM270 | 68 +-
src/jaligner/matrix/matrices/PAM280 | 68 +-
src/jaligner/matrix/matrices/PAM290 | 68 +-
src/jaligner/matrix/matrices/PAM30 | 68 +-
src/jaligner/matrix/matrices/PAM300 | 68 +-
src/jaligner/matrix/matrices/PAM310 | 68 +-
src/jaligner/matrix/matrices/PAM320 | 68 +-
src/jaligner/matrix/matrices/PAM330 | 68 +-
src/jaligner/matrix/matrices/PAM340 | 68 +-
src/jaligner/matrix/matrices/PAM350 | 68 +-
src/jaligner/matrix/matrices/PAM360 | 68 +-
src/jaligner/matrix/matrices/PAM370 | 68 +-
src/jaligner/matrix/matrices/PAM380 | 68 +-
src/jaligner/matrix/matrices/PAM390 | 68 +-
src/jaligner/matrix/matrices/PAM40 | 68 +-
src/jaligner/matrix/matrices/PAM400 | 68 +-
src/jaligner/matrix/matrices/PAM410 | 68 +-
src/jaligner/matrix/matrices/PAM420 | 68 +-
src/jaligner/matrix/matrices/PAM430 | 68 +-
src/jaligner/matrix/matrices/PAM440 | 68 +-
src/jaligner/matrix/matrices/PAM450 | 68 +-
src/jaligner/matrix/matrices/PAM460 | 68 +-
src/jaligner/matrix/matrices/PAM470 | 68 +-
src/jaligner/matrix/matrices/PAM480 | 68 +-
src/jaligner/matrix/matrices/PAM490 | 68 +-
src/jaligner/matrix/matrices/PAM50 | 68 +-
src/jaligner/matrix/matrices/PAM500 | 68 +-
src/jaligner/matrix/matrices/PAM60 | 68 +-
src/jaligner/matrix/matrices/PAM70 | 68 +-
src/jaligner/matrix/matrices/PAM80 | 68 +-
src/jaligner/matrix/matrices/PAM90 | 68 +-
src/jaligner/matrix/package.html | 4 +-
src/jaligner/package.html | 4 +-
src/jaligner/test/AlignmentScoreChecker.java | 131 ---
src/jaligner/test/NeedlemanWunschGotohTester.java | 130 +++
src/jaligner/test/NeedlemanWunschTester.java | 128 ++
src/jaligner/test/RandomSequenceGenerator.java | 30 +-
src/jaligner/test/SmithWatermanGotohTester.java | 130 +++
src/jaligner/test/package.html | 2 +-
src/jaligner/ui/AlignCommandLine.java | 6 +-
src/jaligner/ui/AlignWindow.form | 51 +-
src/jaligner/ui/AlignWindow.java | 146 +--
src/jaligner/ui/clipboard/ClipboardHandler.java | 4 +-
src/jaligner/ui/clipboard/ClipboardHandlerAWT.java | 4 +-
.../ui/clipboard/ClipboardHandlerFactory.java | 4 +-
.../ui/clipboard/ClipboardHandlerJNLP.java | 4 +-
src/jaligner/ui/clipboard/ClipboardListener.java | 4 +-
src/jaligner/ui/clipboard/ClipboardPoller.java | 4 +-
src/jaligner/ui/clipboard/package.html | 4 +-
src/jaligner/ui/filechooser/FileChooser.java | 4 +-
.../ui/filechooser/FileChooserException.java | 4 +-
.../ui/filechooser/FileChooserFactory.java | 4 +-
src/jaligner/ui/filechooser/FileChooserJNLP.java | 4 +-
.../ui/filechooser/FileChooserTrusted.java | 4 +-
src/jaligner/ui/filechooser/NamedInputStream.java | 4 +-
src/jaligner/ui/filechooser/package.html | 4 +-
src/jaligner/ui/images/ToolbarIcons.java | 5 +-
src/jaligner/ui/images/package.html | 4 +-
src/jaligner/ui/logging/DocumentHandler.java | 4 +-
src/jaligner/ui/logging/RecordFormatter.java | 4 +-
src/jaligner/ui/logging/package.html | 4 +-
src/jaligner/ui/package.html | 4 +-
src/jaligner/ui/util/PrintJobMointor.java | 4 +-
src/jaligner/ui/util/TextComponentUtil.java | 4 +-
.../ui/util/TextComponentUtilException.java | 4 +-
src/jaligner/ui/util/package.html | 4 +-
src/jaligner/util/Commons.java | 14 +-
src/jaligner/util/SequenceParser.java | 10 +-
src/jaligner/util/SequenceParserException.java | 4 +-
src/jaligner/util/package.html | 4 +-
384 files changed, 4649 insertions(+), 38093 deletions(-)
diff --git a/README b/README
index d6b7b97..5092535 100644
--- a/README
+++ b/README
@@ -1,3 +1 @@
-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.
+JAligner is an open-source Java implementation of the Needleman–Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..23ff1cd
--- /dev/null
+++ b/README.md
@@ -0,0 +1,2 @@
+**JAligner** is an open-source Java implementation of the [Needleman–Wunsch](http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm) and [Smith-Waterman](http://en.wikipedia.org/wiki/Smith-Waterman_algorithm) algorithms for biological pairwise [sequence alignment](http://en.wikipedia.org/wiki/Sequence_alignment) with the affine gap penalty model.
+
diff --git a/api/allclasses-frame.html b/api/allclasses-frame.html
deleted file mode 100644
index f2bc052..0000000
--- a/api/allclasses-frame.html
+++ /dev/null
@@ -1,110 +0,0 @@
-<!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
deleted file mode 100644
index 2e31c1d..0000000
--- a/api/allclasses-noframe.html
+++ /dev/null
@@ -1,110 +0,0 @@
-<!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
deleted file mode 100644
index 235765c..0000000
--- a/api/constant-values.html
+++ /dev/null
@@ -1,298 +0,0 @@
-<!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>
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-</HEAD>
-
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-
-
-<!-- ========= START OF TOP NAVBAR ======= -->
-<A NAME="navbar_top"><!-- --></A>
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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- </TR>
-</TABLE>
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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-<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>
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-<HR>
-
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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- <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>
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- NEXT</FONT></TD>
-<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>');
- }
- //-->
-</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
deleted file mode 100644
index 90dba7a..0000000
--- a/api/deprecated-list.html
+++ /dev/null
@@ -1,134 +0,0 @@
-<!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="">
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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"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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- <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>
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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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- PREV
- NEXT</FONT></TD>
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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- <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="">
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-<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>
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-<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="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
deleted file mode 100644
index 1c081ac..0000000
--- a/api/help-doc.html
+++ /dev/null
@@ -1,193 +0,0 @@
-<!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="">
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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"> <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>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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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>');
- }
- //-->
-</SCRIPT>
-<NOSCRIPT>
- <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
-</NOSCRIPT>
-
-</FONT></TD>
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-<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="">
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-<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>
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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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- <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
deleted file mode 100644
index 0dde66b..0000000
--- a/api/index-all.html
+++ /dev/null
@@ -1,798 +0,0 @@
-<!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="">
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-<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>
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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>
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-
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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>
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-<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">
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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>
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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/index.html b/api/index.html
deleted file mode 100644
index 9491146..0000000
--- a/api/index.html
+++ /dev/null
@@ -1,26 +0,0 @@
-<!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
deleted file mode 100644
index 6ec4b14..0000000
--- a/api/jaligner.css
+++ /dev/null
@@ -1,38 +0,0 @@
-/* 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
deleted file mode 100644
index 2c86f4f..0000000
--- a/api/jaligner/Alignment.html
+++ /dev/null
@@ -1,891 +0,0 @@
-<!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">
-
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-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
deleted file mode 100644
index 6322e35..0000000
--- a/api/jaligner/Cell.html
+++ /dev/null
@@ -1,385 +0,0 @@
-<!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
deleted file mode 100644
index bc7e865..0000000
--- a/api/jaligner/Directions.html
+++ /dev/null
@@ -1,321 +0,0 @@
-<!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
deleted file mode 100644
index 7fae6a8..0000000
--- a/api/jaligner/Markups.html
+++ /dev/null
@@ -1,321 +0,0 @@
-<!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>
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</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>
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-</TD>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../jaligner/Directions.html" title="class in jaligner"><B>PREV CLASS</B></A>
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-<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>
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- 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>
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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/Sequence.html b/api/jaligner/Sequence.html
deleted file mode 100644
index 04b374a..0000000
--- a/api/jaligner/Sequence.html
+++ /dev/null
@@ -1,635 +0,0 @@
-<!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="">
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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/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="">
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- <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>
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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">
- <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>
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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-<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
deleted file mode 100644
index 44dfd01..0000000
--- a/api/jaligner/SmithWatermanGotoh.html
+++ /dev/null
@@ -1,247 +0,0 @@
-<!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
deleted file mode 100644
index a38c154..0000000
--- a/api/jaligner/class-use/Alignment.html
+++ /dev/null
@@ -1,229 +0,0 @@
-<!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
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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- <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
deleted file mode 100644
index 8e63c82..0000000
--- a/api/jaligner/class-use/Cell.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index f9fa532..0000000
--- a/api/jaligner/class-use/Directions.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index f48ebb0..0000000
--- a/api/jaligner/class-use/Markups.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-</TABLE>
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-</TD>
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- <!--
- if(window==top) {
- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
- }
- //-->
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-<!-- ========= END OF TOP NAVBAR ========= -->
-
-<HR>
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-<B>Uses of Class<br>jaligner.Markups</B></H2>
-</CENTER>
-No usage of jaligner.Markups
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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-</NOSCRIPT>
-
-</FONT></TD>
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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/class-use/Sequence.html b/api/jaligner/class-use/Sequence.html
deleted file mode 100644
index bbe3dee..0000000
--- a/api/jaligner/class-use/Sequence.html
+++ /dev/null
@@ -1,242 +0,0 @@
-<!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="">
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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="../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>
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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">
- <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>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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-<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
deleted file mode 100644
index bd8d4e2..0000000
--- a/api/jaligner/class-use/SmithWatermanGotoh.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index 2634eea..0000000
--- a/api/jaligner/example/Example.html
+++ /dev/null
@@ -1,307 +0,0 @@
-<!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>
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- <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>
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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 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
deleted file mode 100644
index b9c936b..0000000
--- a/api/jaligner/example/class-use/Example.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index 1ab45f8..0000000
--- a/api/jaligner/example/package-frame.html
+++ /dev/null
@@ -1,32 +0,0 @@
-<!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>
-
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-<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
deleted file mode 100644
index 03c32a1..0000000
--- a/api/jaligner/example/package-summary.html
+++ /dev/null
@@ -1,168 +0,0 @@
-<!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();">
-
-
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-<A NAME="navbar_top"><!-- --></A>
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-<A NAME="navbar_top_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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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">
- <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>
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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>
-
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-</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="">
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-<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
deleted file mode 100644
index 63c3ed5..0000000
--- a/api/jaligner/example/package-tree.html
+++ /dev/null
@@ -1,145 +0,0 @@
-<!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="">
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-<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>
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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_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>
-
-
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-<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="">
- <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="../../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>
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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_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
deleted file mode 100644
index 8b8b603..0000000
--- a/api/jaligner/example/package-use.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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="">
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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="#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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- <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>
-
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-</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="">
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-<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>
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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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- <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">
- PREV
- NEXT</FONT></TD>
-<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>');
- }
- //-->
-</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
deleted file mode 100644
index 4c9b4a9..0000000
--- a/api/jaligner/formats/CLUSTAL.html
+++ /dev/null
@@ -1,322 +0,0 @@
-<!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
deleted file mode 100644
index d0e94bb..0000000
--- a/api/jaligner/formats/FASTA.html
+++ /dev/null
@@ -1,302 +0,0 @@
-<!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
deleted file mode 100644
index e2fa269..0000000
--- a/api/jaligner/formats/Format.html
+++ /dev/null
@@ -1,309 +0,0 @@
-<!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
deleted file mode 100644
index 6c924a8..0000000
--- a/api/jaligner/formats/FormatFactory.html
+++ /dev/null
@@ -1,301 +0,0 @@
-<!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>
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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/formats/Format.html" title="class in jaligner.formats"><B>PREV CLASS</B></A>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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-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>
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-<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>
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-<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>
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- <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>
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- <!--
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- }
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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/formats/Pair.html b/api/jaligner/formats/Pair.html
deleted file mode 100644
index 082eafd..0000000
--- a/api/jaligner/formats/Pair.html
+++ /dev/null
@@ -1,278 +0,0 @@
-<!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 ======= -->
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-</TABLE>
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-</TD>
-</TR>
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-<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 =========== -->
-
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->
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-<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">
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-<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 =========== -->
-
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-<!-- ========= CONSTRUCTOR DETAIL ======== -->
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-<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 ========= -->
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-
-</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
deleted file mode 100644
index 36b8354..0000000
--- a/api/jaligner/formats/class-use/CLUSTAL.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index 04e0481..0000000
--- a/api/jaligner/formats/class-use/FASTA.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index 63eec93..0000000
--- a/api/jaligner/formats/class-use/Format.html
+++ /dev/null
@@ -1,220 +0,0 @@
-<!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>
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-<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
deleted file mode 100644
index 4b69f35..0000000
--- a/api/jaligner/formats/class-use/FormatFactory.html
+++ /dev/null
@@ -1,172 +0,0 @@
-<!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
deleted file mode 100644
index 8c57367..0000000
--- a/api/jaligner/formats/class-use/Pair.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index 464aed5..0000000
--- a/api/jaligner/formats/package-frame.html
+++ /dev/null
@@ -1,40 +0,0 @@
-<!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
deleted file mode 100644
index d9ffa95..0000000
--- a/api/jaligner/formats/package-summary.html
+++ /dev/null
@@ -1,183 +0,0 @@
-<!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>
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</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">
- <A HREF="../../jaligner/example/package-summary.html"><B>PREV PACKAGE</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>
-<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="">
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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="#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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- </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
deleted file mode 100644
index 7818733..0000000
--- a/api/jaligner/formats/package-tree.html
+++ /dev/null
@@ -1,147 +0,0 @@
-<!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="">
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-<A NAME="navbar_top_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
- <TR ALIGN="center" VALIGN="top">
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- <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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- </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>
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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>
-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>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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- <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/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_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
deleted file mode 100644
index 48485e9..0000000
--- a/api/jaligner/formats/package-use.html
+++ /dev/null
@@ -1,168 +0,0 @@
-<!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>
-<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="#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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- <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>
-
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-
-<HR>
-<CENTER>
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-<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>
-<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"> <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>
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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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- <!--
- if(window==top) {
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-
-<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
deleted file mode 100644
index 41ec205..0000000
--- a/api/jaligner/matrix/MatricesCompartor.html
+++ /dev/null
@@ -1,277 +0,0 @@
-<!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)";
-}
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-
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-<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 ======== -->
-
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-<!-- =========== FIELD SUMMARY =========== -->
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->
-
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-<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>
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-<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 =========== -->
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-
-<!-- ========= CONSTRUCTOR DETAIL ======== -->
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-<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>
-
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->
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-<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
deleted file mode 100644
index edcdfb4..0000000
--- a/api/jaligner/matrix/Matrix.html
+++ /dev/null
@@ -1,317 +0,0 @@
-<!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>
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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-<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
-</TD>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../jaligner/matrix/MatricesCompartor.html" title="class in jaligner.matrix"><B>PREV CLASS</B></A>
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-<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>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../index.html" target="_top"><B>FRAMES</B></A>
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->
-
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-<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 [...]
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diff --git a/api/jaligner/matrix/MatrixLoader.html b/api/jaligner/matrix/MatrixLoader.html
deleted file mode 100644
index 6994109..0000000
--- a/api/jaligner/matrix/MatrixLoader.html
+++ /dev/null
@@ -1,342 +0,0 @@
-<!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">
-
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-function windowTitle()
-{
- parent.document.title="MatrixLoader (JAligner)";
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-<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 ======== -->
-
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-<!-- =========== FIELD SUMMARY =========== -->
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-<!-- ======== CONSTRUCTOR SUMMARY ======== -->
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-<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="">
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-<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="">
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-<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>
-
-
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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 [...]
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-</HTML>
diff --git a/api/jaligner/matrix/MatrixLoaderException.html b/api/jaligner/matrix/MatrixLoaderException.html
deleted file mode 100644
index 5aab9dd..0000000
--- a/api/jaligner/matrix/MatrixLoaderException.html
+++ /dev/null
@@ -1,238 +0,0 @@
-<!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();">
-
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- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
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-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 ======== -->
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-<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>
-
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- </TD>
-</TR>
-</TABLE>
-
-<!-- ========== METHOD SUMMARY =========== -->
-
-<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
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-<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 =========== -->
-
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-<!-- ========= CONSTRUCTOR DETAIL ======== -->
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-<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 ========== -->
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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/matrix/class-use/MatricesCompartor.html b/api/jaligner/matrix/class-use/MatricesCompartor.html
deleted file mode 100644
index 573acb8..0000000
--- a/api/jaligner/matrix/class-use/MatricesCompartor.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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();">
-
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-<!-- ========= START OF TOP NAVBAR ======= -->
-<A NAME="navbar_top"><!-- --></A>
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- </TR>
-</TABLE>
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-<CENTER>
-<H2>
-<B>Uses of Class<br>jaligner.matrix.MatricesCompartor</B></H2>
-</CENTER>
-No usage of jaligner.matrix.MatricesCompartor
-<P>
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- <SCRIPT type="text/javascript">
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-<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
deleted file mode 100644
index 4449af9..0000000
--- a/api/jaligner/matrix/class-use/Matrix.html
+++ /dev/null
@@ -1,237 +0,0 @@
-<!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();">
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-<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>
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- <!--
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-</NOSCRIPT>
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-</FONT></TD>
-</TR>
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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/matrix/class-use/MatrixLoader.html b/api/jaligner/matrix/class-use/MatrixLoader.html
deleted file mode 100644
index 9fb9197..0000000
--- a/api/jaligner/matrix/class-use/MatrixLoader.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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- </TR>
-</TABLE>
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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-</TD>
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- <SCRIPT type="text/javascript">
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-
-<HR>
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-<B>Uses of Class<br>jaligner.matrix.MatrixLoader</B></H2>
-</CENTER>
-No usage of jaligner.matrix.MatrixLoader
-<P>
-<HR>
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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-</TABLE>
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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>');
- }
- //-->
-</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
deleted file mode 100644
index 11d1186..0000000
--- a/api/jaligner/matrix/class-use/MatrixLoaderException.html
+++ /dev/null
@@ -1,196 +0,0 @@
-<!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="">
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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"> <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>
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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- </TR>
-</TABLE>
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
-</TD>
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- <!--
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- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
-</NOSCRIPT>
-
-</FONT></TD>
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-</TABLE>
-<A NAME="skip-navbar_top"></A>
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-
-<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="">
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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-</TABLE>
-</TD>
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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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/matrix/package-frame.html b/api/jaligner/matrix/package-frame.html
deleted file mode 100644
index fc579b3..0000000
--- a/api/jaligner/matrix/package-frame.html
+++ /dev/null
@@ -1,47 +0,0 @@
-<!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">
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-
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-<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">
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deleted file mode 100644
index 20e73a5..0000000
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+++ /dev/null
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-Package jaligner.matrix
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-Scoring matrices package.
-<P>
-<B>See:</B>
-<BR>
- <A HREF="#package_description"><B>Description</B></A>
-<P>
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-<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>
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-<A NAME="package_description"><!-- --></A><H2>
-Package jaligner.matrix Description
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-<P>
-Scoring matrices package.
-<P>
-
-<P>
-<DL>
-<DT><B>Author:</B></DT>
- <DD>Ahmed Moustafa (ahmed at users.sf.net)</DD>
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deleted file mode 100644
index bc71906..0000000
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+++ /dev/null
@@ -1,152 +0,0 @@
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-<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)
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diff --git a/api/jaligner/matrix/package-use.html b/api/jaligner/matrix/package-use.html
deleted file mode 100644
index 509ee6b..0000000
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+++ /dev/null
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-Packages that use <A HREF="../../jaligner/matrix/package-summary.html">jaligner.matrix</A></FONT></TD>
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-<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>
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-<A NAME="jaligner"><!-- --></A>
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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-<TD><B><A HREF="../../jaligner/matrix/class-use/Matrix.html#jaligner"><B>Matrix</B></A></B>
-
-<BR>
- Scoring matrix.</TD>
-</TR>
-</TABLE>
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-<A NAME="jaligner.matrix"><!-- --></A>
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-<TD><B><A HREF="../../jaligner/matrix/class-use/Matrix.html#jaligner.matrix"><B>Matrix</B></A></B>
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- Scoring matrix.</TD>
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-<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
deleted file mode 100644
index f02e5c4..0000000
--- a/api/jaligner/package-frame.html
+++ /dev/null
@@ -1,42 +0,0 @@
-<!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
deleted file mode 100644
index 034b10a..0000000
--- a/api/jaligner/package-summary.html
+++ /dev/null
@@ -1,188 +0,0 @@
-<!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
deleted file mode 100644
index 6168855..0000000
--- a/api/jaligner/package-tree.html
+++ /dev/null
@@ -1,146 +0,0 @@
-<!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
deleted file mode 100644
index fc31388..0000000
--- a/api/jaligner/package-use.html
+++ /dev/null
@@ -1,212 +0,0 @@
-<!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>
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-<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>
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-<P>
-<A NAME="jaligner"><!-- --></A>
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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-</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="">
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-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">
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-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>
-
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-<HR>
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-<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 [...]
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diff --git a/api/jaligner/test/AlignmentScoreChecker.html b/api/jaligner/test/AlignmentScoreChecker.html
deleted file mode 100644
index 34d55db..0000000
--- a/api/jaligner/test/AlignmentScoreChecker.html
+++ /dev/null
@@ -1,260 +0,0 @@
-<!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>
-
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-function windowTitle()
-{
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-}
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-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>
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-<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>
-
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-<B>Method Summary</B></FONT></TD>
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-<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="">
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-<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>
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-<!-- ============ FIELD DETAIL =========== -->
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-<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 ========== -->
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-<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>
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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 [...]
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diff --git a/api/jaligner/test/RandomSequenceGenerator.html b/api/jaligner/test/RandomSequenceGenerator.html
deleted file mode 100644
index f487be4..0000000
--- a/api/jaligner/test/RandomSequenceGenerator.html
+++ /dev/null
@@ -1,284 +0,0 @@
-<!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>
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-<HR>
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-<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>
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-<TD><CODE><B><A HREF="../../jaligner/test/RandomSequenceGenerator.html#RandomSequenceGenerator()">RandomSequenceGenerator</A></B>()</CODE>
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-<TD><CODE><B><A HREF="../../jaligner/test/RandomSequenceGenerator.html#generate(int)">generate</A></B>(int length)</CODE>
-
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- Returns random sequence</TD>
-</TR>
-<TR BGCOLOR="white" CLASS="TableRowColor">
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-<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>
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- <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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-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 ========= -->
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diff --git a/api/jaligner/test/class-use/AlignmentScoreChecker.html b/api/jaligner/test/class-use/AlignmentScoreChecker.html
deleted file mode 100644
index c047635..0000000
--- a/api/jaligner/test/class-use/AlignmentScoreChecker.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<HTML>
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-<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
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-Uses of Class jaligner.test.AlignmentScoreChecker (JAligner)
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diff --git a/api/jaligner/test/class-use/RandomSequenceGenerator.html b/api/jaligner/test/class-use/RandomSequenceGenerator.html
deleted file mode 100644
index b623901..0000000
--- a/api/jaligner/test/class-use/RandomSequenceGenerator.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<HTML>
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-Uses of Class jaligner.test.RandomSequenceGenerator (JAligner)
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-<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
deleted file mode 100644
index f364935..0000000
--- a/api/jaligner/test/package-frame.html
+++ /dev/null
@@ -1,34 +0,0 @@
-<!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
deleted file mode 100644
index 6bb4b5e..0000000
--- a/api/jaligner/test/package-summary.html
+++ /dev/null
@@ -1,171 +0,0 @@
-<!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="">
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</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">
- <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">
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- <A HREF="package-summary.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>
-</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>
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- </TR>
-</TABLE>
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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/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
deleted file mode 100644
index 2ea01ac..0000000
--- a/api/jaligner/test/package-tree.html
+++ /dev/null
@@ -1,145 +0,0 @@
-<!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="">
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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- <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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- <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">
- <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">
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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.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>
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-</TABLE>
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-</TR>
-
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- <A HREF="../../jaligner/matrix/package-tree.html"><B>PREV</B></A>
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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_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
deleted file mode 100644
index 764a231..0000000
--- a/api/jaligner/test/package-use.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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();">
-
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-<!-- ========= START OF TOP NAVBAR ======= -->
-<A NAME="navbar_top"><!-- --></A>
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- </TR>
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-<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
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-No usage of jaligner.test
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- <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
deleted file mode 100644
index 4a4b2e0..0000000
--- a/api/jaligner/ui/AlignCommandLine.html
+++ /dev/null
@@ -1,260 +0,0 @@
-<!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
deleted file mode 100644
index 9bfa4d2..0000000
--- a/api/jaligner/ui/AlignWindow.html
+++ /dev/null
@@ -1,569 +0,0 @@
-<!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="">
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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="#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>
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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>
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-
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-<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>
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- <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>
-</NOSCRIPT>
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-<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>
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-<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 [...]
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-</HTML>
diff --git a/api/jaligner/ui/class-use/AlignCommandLine.html b/api/jaligner/ui/class-use/AlignCommandLine.html
deleted file mode 100644
index 2c64220..0000000
--- a/api/jaligner/ui/class-use/AlignCommandLine.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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 ======= -->
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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- <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
- 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="">
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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-</NOSCRIPT>
-
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-</TR>
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-<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
deleted file mode 100644
index eddc952..0000000
--- a/api/jaligner/ui/class-use/AlignWindow.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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="">
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-<A NAME="navbar_top_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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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="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>
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-</NOSCRIPT>
-
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-</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>
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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">
- <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
deleted file mode 100644
index 4317186..0000000
--- a/api/jaligner/ui/clipboard/ClipboardHandler.html
+++ /dev/null
@@ -1,248 +0,0 @@
-<!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="">
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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="#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>
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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">
- 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
deleted file mode 100644
index 788cfca..0000000
--- a/api/jaligner/ui/clipboard/ClipboardHandlerAWT.html
+++ /dev/null
@@ -1,293 +0,0 @@
-<!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>
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- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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-<!-- ========= 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
deleted file mode 100644
index 72bc1a3..0000000
--- a/api/jaligner/ui/clipboard/ClipboardHandlerFactory.html
+++ /dev/null
@@ -1,236 +0,0 @@
-<!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>
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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/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>
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- 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>
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- 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
deleted file mode 100644
index d00caa3..0000000
--- a/api/jaligner/ui/clipboard/ClipboardHandlerJNLP.html
+++ /dev/null
@@ -1,293 +0,0 @@
-<!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>
-
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-
-<SCRIPT type="text/javascript">
-function windowTitle()
-{
- parent.document.title="ClipboardHandlerJNLP (JAligner)";
-}
-</SCRIPT>
-
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-
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-</TD>
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- <A HREF="../../../jaligner/ui/clipboard/ClipboardHandlerFactory.html" title="class in jaligner.ui.clipboard"><B>PREV CLASS</B></A>
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-<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 ======== -->
-
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-<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="">
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
- <TR ALIGN="center" VALIGN="top">
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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="#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>
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- 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>
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-<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
deleted file mode 100644
index f3876af..0000000
--- a/api/jaligner/ui/clipboard/ClipboardListener.html
+++ /dev/null
@@ -1,225 +0,0 @@
-<!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>
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- 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="">
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>
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- <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"> <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>
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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>
-
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-<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>
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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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- }
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-
-<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
deleted file mode 100644
index 8a2d0c9..0000000
--- a/api/jaligner/ui/clipboard/ClipboardPoller.html
+++ /dev/null
@@ -1,314 +0,0 @@
-<!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
deleted file mode 100644
index 5f6d823..0000000
--- a/api/jaligner/ui/clipboard/class-use/ClipboardHandler.html
+++ /dev/null
@@ -1,196 +0,0 @@
-<!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>
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- </TR>
-</TABLE>
-</TD>
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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-</TD>
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-<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>');
- }
- //-->
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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/clipboard/class-use/ClipboardHandlerAWT.html b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerAWT.html
deleted file mode 100644
index 184085e..0000000
--- a/api/jaligner/ui/clipboard/class-use/ClipboardHandlerAWT.html
+++ /dev/null
@@ -1,136 +0,0 @@
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-<!--NewPage-->
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-<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="">
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-<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
-<A NAME="navbar_top_firstrow"><!-- --></A>
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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/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>
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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">
- 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="">
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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/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>
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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">
- 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>');
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- //-->
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-<NOSCRIPT>
- <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
-</NOSCRIPT>
-
-</FONT></TD>
-</TR>
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-<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
deleted file mode 100644
index 40a9a41..0000000
--- a/api/jaligner/ui/clipboard/class-use/ClipboardHandlerFactory.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
-<A NAME="navbar_top_firstrow"><!-- --></A>
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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/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>
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- <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="">
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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-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>
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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">
- 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>');
- }
- //-->
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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/clipboard/class-use/ClipboardHandlerJNLP.html b/api/jaligner/ui/clipboard/class-use/ClipboardHandlerJNLP.html
deleted file mode 100644
index 9d11863..0000000
--- a/api/jaligner/ui/clipboard/class-use/ClipboardHandlerJNLP.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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="">
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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"> <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="">
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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"> <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>
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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">
- 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
deleted file mode 100644
index e96f0eb..0000000
--- a/api/jaligner/ui/clipboard/class-use/ClipboardListener.html
+++ /dev/null
@@ -1,199 +0,0 @@
-<!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
deleted file mode 100644
index 4838e8f..0000000
--- a/api/jaligner/ui/clipboard/class-use/ClipboardPoller.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index ede0c46..0000000
--- a/api/jaligner/ui/clipboard/package-frame.html
+++ /dev/null
@@ -1,51 +0,0 @@
-<!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
deleted file mode 100644
index 761e691..0000000
--- a/api/jaligner/ui/clipboard/package-summary.html
+++ /dev/null
@@ -1,198 +0,0 @@
-<!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
deleted file mode 100644
index df3711f..0000000
--- a/api/jaligner/ui/clipboard/package-tree.html
+++ /dev/null
@@ -1,155 +0,0 @@
-<!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
deleted file mode 100644
index 1b9ad65..0000000
--- a/api/jaligner/ui/clipboard/package-use.html
+++ /dev/null
@@ -1,188 +0,0 @@
-<!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">
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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>
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-<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="">
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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>
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-
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- PREV
- NEXT</FONT></TD>
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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- 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>
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-<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
deleted file mode 100644
index 9805838..0000000
--- a/api/jaligner/ui/filechooser/FileChooser.html
+++ /dev/null
@@ -1,372 +0,0 @@
-<!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="">
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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="#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>
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- 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
deleted file mode 100644
index 87e22df..0000000
--- a/api/jaligner/ui/filechooser/FileChooserException.html
+++ /dev/null
@@ -1,242 +0,0 @@
-<!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">
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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>
-<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>
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
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-
-<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>
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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 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
deleted file mode 100644
index bc355d2..0000000
--- a/api/jaligner/ui/filechooser/FileChooserFactory.html
+++ /dev/null
@@ -1,236 +0,0 @@
-<!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>
-
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-<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>
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- SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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-</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>
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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/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>
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- 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
deleted file mode 100644
index ee9ca87..0000000
--- a/api/jaligner/ui/filechooser/FileChooserJNLP.html
+++ /dev/null
@@ -1,325 +0,0 @@
-<!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>
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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">
- <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
deleted file mode 100644
index d15bb5e..0000000
--- a/api/jaligner/ui/filechooser/FileChooserTrusted.html
+++ /dev/null
@@ -1,325 +0,0 @@
-<!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
deleted file mode 100644
index 8fa6ff3..0000000
--- a/api/jaligner/ui/filechooser/NamedInputStream.html
+++ /dev/null
@@ -1,288 +0,0 @@
-<!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
deleted file mode 100644
index 509f76b..0000000
--- a/api/jaligner/ui/filechooser/class-use/FileChooser.html
+++ /dev/null
@@ -1,196 +0,0 @@
-<!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
deleted file mode 100644
index 3af6a3b..0000000
--- a/api/jaligner/ui/filechooser/class-use/FileChooserException.html
+++ /dev/null
@@ -1,215 +0,0 @@
-<!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
deleted file mode 100644
index 2fe5870..0000000
--- a/api/jaligner/ui/filechooser/class-use/FileChooserFactory.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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">
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- <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">
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- </TR>
-</TABLE>
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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>');
- }
- //-->
-</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
deleted file mode 100644
index 86c4642..0000000
--- a/api/jaligner/ui/filechooser/class-use/FileChooserJNLP.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index bbb4eab..0000000
--- a/api/jaligner/ui/filechooser/class-use/FileChooserTrusted.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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
deleted file mode 100644
index 6f5aed1..0000000
--- a/api/jaligner/ui/filechooser/class-use/NamedInputStream.html
+++ /dev/null
@@ -1,217 +0,0 @@
-<!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
deleted file mode 100644
index d3bd8e4..0000000
--- a/api/jaligner/ui/filechooser/package-frame.html
+++ /dev/null
@@ -1,51 +0,0 @@
-<!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
deleted file mode 100644
index 098aacb..0000000
--- a/api/jaligner/ui/filechooser/package-summary.html
+++ /dev/null
@@ -1,197 +0,0 @@
-<!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
deleted file mode 100644
index 1507051..0000000
--- a/api/jaligner/ui/filechooser/package-tree.html
+++ /dev/null
@@ -1,153 +0,0 @@
-<!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
deleted file mode 100644
index d4f3d26..0000000
--- a/api/jaligner/ui/filechooser/package-use.html
+++ /dev/null
@@ -1,193 +0,0 @@
-<!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
deleted file mode 100644
index 6d27da6..0000000
--- a/api/jaligner/ui/images/ToolbarIcons.html
+++ /dev/null
@@ -1,441 +0,0 @@
-<!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 ====== -->
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- <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 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
deleted file mode 100644
index 7d24619..0000000
--- a/api/jaligner/ui/images/class-use/ToolbarIcons.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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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="../../../../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
deleted file mode 100644
index e73580e..0000000
--- a/api/jaligner/ui/images/package-frame.html
+++ /dev/null
@@ -1,32 +0,0 @@
-<!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
deleted file mode 100644
index 14e8da4..0000000
--- a/api/jaligner/ui/images/package-summary.html
+++ /dev/null
@@ -1,167 +0,0 @@
-<!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="">
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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>
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- <A HREF="../../../jaligner/ui/filechooser/package-summary.html"><B>PREV PACKAGE</B></A>
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- if(window==top) {
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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/ui/images/package-tree.html b/api/jaligner/ui/images/package-tree.html
deleted file mode 100644
index 110c01e..0000000
--- a/api/jaligner/ui/images/package-tree.html
+++ /dev/null
@@ -1,145 +0,0 @@
-<!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>
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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- </TR>
-</TABLE>
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-<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>
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- <!--
- if(window==top) {
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- }
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-
-<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>
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- </TR>
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-<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>
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- <!--
- if(window==top) {
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
- }
- //-->
-</SCRIPT>
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- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
-</NOSCRIPT>
-
-</FONT></TD>
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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/ui/images/package-use.html b/api/jaligner/ui/images/package-use.html
deleted file mode 100644
index a25559d..0000000
--- a/api/jaligner/ui/images/package-use.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-<A NAME="navbar_top_firstrow"><!-- --></A>
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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- </TR>
-</TABLE>
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-<a href="http://jaligner.sourceforge.net">JAligner</a></EM>
-</TD>
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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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- <SCRIPT type="text/javascript">
- <!--
- if(window==top) {
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
- }
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-<!-- ========= END OF TOP NAVBAR ========= -->
-
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-<CENTER>
-<H2>
-<B>Uses of Package<br>jaligner.ui.images</B></H2>
-</CENTER>
-No usage of jaligner.ui.images
-<P>
-<HR>
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-<A NAME="navbar_bottom"><!-- --></A>
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- </TR>
-</TABLE>
-</TD>
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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-</TD>
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- PREV
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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- <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
deleted file mode 100644
index d41d1dc..0000000
--- a/api/jaligner/ui/logging/DocumentHandler.html
+++ /dev/null
@@ -1,310 +0,0 @@
-<!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>
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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">
- 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>
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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-
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-<!-- ======== 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
deleted file mode 100644
index 4a1fc4e..0000000
--- a/api/jaligner/ui/logging/RecordFormatter.html
+++ /dev/null
@@ -1,318 +0,0 @@
-<!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
deleted file mode 100644
index 8d264de..0000000
--- a/api/jaligner/ui/logging/class-use/DocumentHandler.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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- <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>
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- <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>');
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-
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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/ui/logging/class-use/RecordFormatter.html b/api/jaligner/ui/logging/class-use/RecordFormatter.html
deleted file mode 100644
index 0508514..0000000
--- a/api/jaligner/ui/logging/class-use/RecordFormatter.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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 ======= -->
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- <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>
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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>
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-<TR>
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- PREV
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- <A HREF="RecordFormatter.html" target="_top"><B>NO FRAMES</B></A>
- <SCRIPT type="text/javascript">
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-</FONT></TD>
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-</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>
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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/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>
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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">
- 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>');
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- //-->
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- <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>
-</NOSCRIPT>
-
-</FONT></TD>
-</TR>
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-<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
deleted file mode 100644
index a2b2fd7..0000000
--- a/api/jaligner/ui/logging/package-frame.html
+++ /dev/null
@@ -1,34 +0,0 @@
-<!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>
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-<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="">
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-<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
deleted file mode 100644
index e7f93c4..0000000
--- a/api/jaligner/ui/logging/package-summary.html
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-<META NAME="keywords" CONTENT="jaligner.ui.logging package">
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-<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="">
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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>
- <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>
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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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_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="">
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- <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>
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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_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
deleted file mode 100644
index 7246028..0000000
--- a/api/jaligner/ui/logging/package-tree.html
+++ /dev/null
@@ -1,149 +0,0 @@
-<!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 ======= -->
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-<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>
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- <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>
-
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../jaligner/ui/images/package-tree.html"><B>PREV</B></A>
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-<HR>
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-Class Hierarchy
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-<UL>
-<LI TYPE="circle">class java.lang.Object<UL>
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-<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
deleted file mode 100644
index c0015cc..0000000
--- a/api/jaligner/ui/logging/package-use.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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)";
-}
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-
-</HEAD>
-
-<BODY BGCOLOR="white" onload="windowTitle();">
-
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-<A NAME="navbar_top"><!-- --></A>
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- </TR>
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-</CENTER>
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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_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
deleted file mode 100644
index eabccef..0000000
--- a/api/jaligner/ui/package-frame.html
+++ /dev/null
@@ -1,34 +0,0 @@
-<!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">
-
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-</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">
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-<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>
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diff --git a/api/jaligner/ui/package-summary.html b/api/jaligner/ui/package-summary.html
deleted file mode 100644
index 321df4b..0000000
--- a/api/jaligner/ui/package-summary.html
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@@ -1,171 +0,0 @@
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
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-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="">
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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-</TD>
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-
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- <A HREF="../../jaligner/test/package-summary.html"><B>PREV PACKAGE</B></A>
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-<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>
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- </TR>
-</TABLE>
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-<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 [...]
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-</HTML>
diff --git a/api/jaligner/ui/package-tree.html b/api/jaligner/ui/package-tree.html
deleted file mode 100644
index fe0dc17..0000000
--- a/api/jaligner/ui/package-tree.html
+++ /dev/null
@@ -1,160 +0,0 @@
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-<!--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)
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-
-
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-{
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-
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-<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 [...]
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diff --git a/api/jaligner/ui/package-use.html b/api/jaligner/ui/package-use.html
deleted file mode 100644
index 10d448b..0000000
--- a/api/jaligner/ui/package-use.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-<HTML>
-<HEAD>
-<!-- Generated by javadoc (build 1.4.2_07) on Tue May 03 15:20:23 PDT 2005 -->
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-Uses of Package jaligner.ui (JAligner)
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../jaligner.css" TITLE="Style">
-
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-}
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diff --git a/api/jaligner/ui/util/PrintJobMointor.html b/api/jaligner/ui/util/PrintJobMointor.html
deleted file mode 100644
index aab1cce..0000000
--- a/api/jaligner/ui/util/PrintJobMointor.html
+++ /dev/null
@@ -1,235 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!--NewPage-->
-<HTML>
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-PrintJobMointor (JAligner)
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-function windowTitle()
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-}
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-<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>
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-<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>
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-</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>
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-<!-- ========= END OF CLASS DATA ========= -->
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-<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
deleted file mode 100644
index 153b40c..0000000
--- a/api/jaligner/ui/util/TextComponentUtil.html
+++ /dev/null
@@ -1,449 +0,0 @@
-<!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="">
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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- <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>
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- </TR>
-</TABLE>
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-</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">
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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-<!-- ========= 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="">
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>
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- </TR>
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-<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>
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- <!--
- if(window==top) {
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- //-->
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-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
deleted file mode 100644
index cb8ca67..0000000
--- a/api/jaligner/ui/util/TextComponentUtilException.html
+++ /dev/null
@@ -1,238 +0,0 @@
-<!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>
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-<A NAME="navbar_top_firstrow"><!-- --></A>
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-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>
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-<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>
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-<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>
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-<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>
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->
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-<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 [...]
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diff --git a/api/jaligner/ui/util/class-use/PrintJobMointor.html b/api/jaligner/ui/util/class-use/PrintJobMointor.html
deleted file mode 100644
index 4cff19c..0000000
--- a/api/jaligner/ui/util/class-use/PrintJobMointor.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-
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-</CENTER>
-No usage of jaligner.ui.util.PrintJobMointor
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diff --git a/api/jaligner/ui/util/class-use/TextComponentUtil.html b/api/jaligner/ui/util/class-use/TextComponentUtil.html
deleted file mode 100644
index 093e4b1..0000000
--- a/api/jaligner/ui/util/class-use/TextComponentUtil.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../jaligner.css" TITLE="Style">
-
-<SCRIPT type="text/javascript">
-function windowTitle()
-{
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-}
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-<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
deleted file mode 100644
index 678e3b6..0000000
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-<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="">
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-<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,
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-<CODE>static boolean</CODE></FONT></TD>
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-
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-<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>
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diff --git a/api/jaligner/ui/util/package-frame.html b/api/jaligner/ui/util/package-frame.html
deleted file mode 100644
index 6117b5a..0000000
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-<A HREF="TextComponentUtil.html" title="class in jaligner.ui.util" target="classFrame">TextComponentUtil</A></FONT></TD>
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diff --git a/api/jaligner/ui/util/package-summary.html b/api/jaligner/ui/util/package-summary.html
deleted file mode 100644
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-<P>
-<B>See:</B>
-<BR>
- <A HREF="#package_description"><B>Description</B></A>
-<P>
-
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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-<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>
-
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-
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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-<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>
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-
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diff --git a/api/jaligner/ui/util/package-tree.html b/api/jaligner/ui/util/package-tree.html
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deleted file mode 100644
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+++ /dev/null
@@ -1,162 +0,0 @@
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-</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>
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diff --git a/api/jaligner/util/Commons.html b/api/jaligner/util/Commons.html
deleted file mode 100644
index 7562fc1..0000000
--- a/api/jaligner/util/Commons.html
+++ /dev/null
@@ -1,394 +0,0 @@
-<!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)";
-}
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-
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-
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-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>
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-<!-- ======== NESTED CLASS SUMMARY ======== -->
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-<B>Constructor Summary</B></FONT></TD>
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-<TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE><B><A HREF="../../jaligner/util/Commons.html#Commons()">Commons</A></B>()</CODE>
-
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- </TD>
-</TR>
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-
-<!-- ========== METHOD SUMMARY =========== -->
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-<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>
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-public static java.lang.String <B>getLineSeparator</B>()</PRE>
-<DL>
-<DD>Returns system line separator.
-<P>
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-<DL>
-<DD>Returns user's current directory.
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-<DD>Sets the JNLP flag to true of false
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-<DL>
-<DD>Returns the current release version of JAligner
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-<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>
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-<DT><B>Returns:</B><DD>information about JAligner</DL>
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->
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-<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 [...]
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diff --git a/api/jaligner/util/SequenceParser.html b/api/jaligner/util/SequenceParser.html
deleted file mode 100644
index e164e71..0000000
--- a/api/jaligner/util/SequenceParser.html
+++ /dev/null
@@ -1,297 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<!--NewPage-->
-<HTML>
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-<!-- 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">
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-<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 ======== -->
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-<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 =========== -->
-
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-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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-<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>
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-<!-- ============ FIELD DETAIL =========== -->
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-<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 ========== -->
-
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-<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 ========= -->
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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 [...]
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diff --git a/api/jaligner/util/SequenceParserException.html b/api/jaligner/util/SequenceParserException.html
deleted file mode 100644
index 38f7b59..0000000
--- a/api/jaligner/util/SequenceParserException.html
+++ /dev/null
@@ -1,238 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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-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>
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-<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>
-
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-</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>
-
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diff --git a/api/jaligner/util/class-use/Commons.html b/api/jaligner/util/class-use/Commons.html
deleted file mode 100644
index d6747f9..0000000
--- a/api/jaligner/util/class-use/Commons.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-<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)";
-}
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diff --git a/api/jaligner/util/class-use/SequenceParser.html b/api/jaligner/util/class-use/SequenceParser.html
deleted file mode 100644
index 78fb9d8..0000000
--- a/api/jaligner/util/class-use/SequenceParser.html
+++ /dev/null
@@ -1,136 +0,0 @@
-<!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>
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-
-<SCRIPT type="text/javascript">
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-}
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-<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 [...]
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deleted file mode 100644
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-<TD><A HREF="#jaligner.util"><B>jaligner.util</B></A></TD>
-<TD>Utility classes for helping core and GUI classes. </TD>
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-<CODE>static <A HREF="../../../jaligner/Sequence.html" title="class in jaligner">Sequence</A></CODE></FONT></TD>
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-
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deleted file mode 100644
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-<BR>
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-<P>
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-<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>
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-<TD WIDTH="15%"><B><A HREF="../../jaligner/util/SequenceParserException.html" title="class in jaligner.util">SequenceParserException</A></B></TD>
-<TD> </TD>
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-
-
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-<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>
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diff --git a/api/overview-summary.html b/api/overview-summary.html
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-<TD>Core classes for the implementation of Smith-Waterman-Gotoh algorithm</TD>
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-<TR BGCOLOR="white" CLASS="TableRowColor">
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-<TD>Scoring matrices package.</TD>
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-<TD>Testing package.</TD>
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-<TD WIDTH="20%"><B><A HREF="jaligner/ui/package-summary.html">jaligner.ui</A></B></TD>
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT> </TD>
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- <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
deleted file mode 100644
index 9a68d44..0000000
--- a/api/overview-tree.html
+++ /dev/null
@@ -1,186 +0,0 @@
-<!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
deleted file mode 100644
index 34b4a0c..0000000
--- a/api/package-list
+++ /dev/null
@@ -1,12 +0,0 @@
-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
deleted file mode 100644
index 1c6efb7..0000000
--- a/api/packages.html
+++ /dev/null
@@ -1,37 +0,0 @@
-<!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
deleted file mode 100644
index c814867..0000000
Binary files a/api/resources/inherit.gif and /dev/null differ
diff --git a/api/serialized-form.html b/api/serialized-form.html
deleted file mode 100644
index 6d1fa02..0000000
--- a/api/serialized-form.html
+++ /dev/null
@@ -1,1232 +0,0 @@
-<!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
index 6a089b0..6902f5e 100644
--- a/build.properties
+++ b/build.properties
@@ -1,18 +1,14 @@
# 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
+class.path = ${classpath}:${java.home}/lib/javaws.jar
# Intermediate directory for building class files.
-build.dir = ./build
+build.dir = ./bin
# Compiler options.
debug = on
@@ -28,7 +24,7 @@ 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 [...]
+javadoc.doc.title = JAligner: Java implementation of Smith-Waterman for biological sequence alignment
+javadoc.header = JAligner
+javadoc.footer =
+javadoc.bottom = <small>By: <a href="http://ahmedmoustafa.com/">Ahmed Moustafa</a> | <a href="http://github.com/ahmedmoustafa/JAligner/">JAligner</a> is licensed under <a href="http://www.opensource.org/licenses/gpl-license">The GNU General Public License (GPL)</a></small>
diff --git a/build.xml b/build.xml
index 21a162f..4112e74 100644
--- a/build.xml
+++ b/build.xml
@@ -1,64 +1,51 @@
<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>
+ <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}" includeantruntime="false">
+ <include name="**/*.java" />
+ </javac>
+ </target>
+ <target name="resources" depends="init" description="Copy non-source code under the build directory">
+ <copy todir="${build.dir}/jaligner/example/sequences">
+ <fileset dir="src/jaligner/example/sequences">
+ </fileset>
+ </copy>
+ <copy todir="${build.dir}/jaligner/matrix/matrices">
+ <fileset dir="src/jaligner/matrix/matrices">
+ </fileset>
+ </copy>
+ <copy todir="${build.dir}/jaligner/ui/images/gifs">
+ <fileset dir="src/jaligner/ui/images/gifs">
+ </fileset>
+ </copy>
+ </target>
+ <target name="jar" depends="compile,resources">
+ <jar jarfile="${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
deleted file mode 100755
index 1738168..0000000
--- a/jaligner.bat
+++ /dev/null
@@ -1 +0,0 @@
-java -jar jaligner.jar
diff --git a/jaligner.css b/jaligner.css
deleted file mode 100644
index 6ec4b14..0000000
--- a/jaligner.css
+++ /dev/null
@@ -1,38 +0,0 @@
-/* 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
index 25ec101..0c880b8 100644
Binary files a/jaligner.jar and b/jaligner.jar differ
diff --git a/jaligner.sh b/jaligner.sh
deleted file mode 100755
index 1738168..0000000
--- a/jaligner.sh
+++ /dev/null
@@ -1 +0,0 @@
-java -jar jaligner.jar
diff --git a/src/NAligner/.cvsignore b/src/NAligner/.cvsignore
deleted file mode 100644
index 4e69665..0000000
--- a/src/NAligner/.cvsignore
+++ /dev/null
@@ -1,13 +0,0 @@
-bin
-obj
-doc
-Releases
-CVSROOT
-*.user
-*.suo
-*.idx
-*.mdx
-*.wdx
-_ReSharper*
-*resharper*
-
diff --git a/src/NAligner/Alignment.cs b/src/NAligner/Alignment.cs
deleted file mode 100644
index cfb2a41..0000000
--- a/src/NAligner/Alignment.cs
+++ /dev/null
@@ -1,244 +0,0 @@
-#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
deleted file mode 100644
index 9502454..0000000
--- a/src/NAligner/AssemblyInfo.cs
+++ /dev/null
@@ -1,79 +0,0 @@
-#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
deleted file mode 100644
index 40a9589..0000000
--- a/src/NAligner/Cell.cs
+++ /dev/null
@@ -1,75 +0,0 @@
-#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
deleted file mode 100644
index 04570ed..0000000
--- a/src/NAligner/Directions.cs
+++ /dev/null
@@ -1,38 +0,0 @@
-#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
deleted file mode 100644
index ac8dead..0000000
--- a/src/NAligner/Markups.cs
+++ /dev/null
@@ -1,39 +0,0 @@
-#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
deleted file mode 100644
index fa82cd1..0000000
--- a/src/NAligner/Matrix.cs
+++ /dev/null
@@ -1,117 +0,0 @@
-#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
deleted file mode 100644
index 53450c5..0000000
--- a/src/NAligner/NAligner.csproj
+++ /dev/null
@@ -1,189 +0,0 @@
-<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
deleted file mode 100644
index 4e9aaa0..0000000
--- a/src/NAligner/NAligner.ndoc
+++ /dev/null
@@ -1,296 +0,0 @@
-<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
deleted file mode 100644
index 141595b..0000000
--- a/src/NAligner/NamespaceDoc.cs
+++ /dev/null
@@ -1,36 +0,0 @@
-#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
deleted file mode 100644
index 5ab73e8..0000000
--- a/src/NAligner/Sequence.cs
+++ /dev/null
@@ -1,283 +0,0 @@
-#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
deleted file mode 100644
index 22a04b0..0000000
--- a/src/NAligner/SmithWatermanGotoh.cs
+++ /dev/null
@@ -1,416 +0,0 @@
-#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
deleted file mode 100644
index fcc6ccb..0000000
--- a/src/NAligner/formats/AlignmentFormatter.cs
+++ /dev/null
@@ -1,44 +0,0 @@
-#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
deleted file mode 100644
index 60f8f0f..0000000
--- a/src/NAligner/formats/CLUSTAL.cs
+++ /dev/null
@@ -1,117 +0,0 @@
-#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
deleted file mode 100644
index 15d3b75..0000000
--- a/src/NAligner/formats/FASTA.cs
+++ /dev/null
@@ -1,70 +0,0 @@
-#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
deleted file mode 100644
index e56eedd..0000000
--- a/src/NAligner/formats/FormatterFactory.cs
+++ /dev/null
@@ -1,72 +0,0 @@
-#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
deleted file mode 100644
index 8007265..0000000
--- a/src/NAligner/formats/NamespaceDoc.cs
+++ /dev/null
@@ -1,29 +0,0 @@
-#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
deleted file mode 100644
index 42f8052..0000000
--- a/src/NAligner/formats/Pair.cs
+++ /dev/null
@@ -1,189 +0,0 @@
-#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
deleted file mode 100644
index 46e9e85..0000000
--- a/src/NAligner/matrices/BLOSUM100
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 81ebd98..0000000
--- a/src/NAligner/matrices/BLOSUM30
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index a6d99f5..0000000
--- a/src/NAligner/matrices/BLOSUM35
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 1a4baa2..0000000
--- a/src/NAligner/matrices/BLOSUM40
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 18c3323..0000000
--- a/src/NAligner/matrices/BLOSUM45
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 3f62e3c..0000000
--- a/src/NAligner/matrices/BLOSUM50
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index c0cf3ff..0000000
--- a/src/NAligner/matrices/BLOSUM55
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 4fd1943..0000000
--- a/src/NAligner/matrices/BLOSUM60
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 205f139..0000000
--- a/src/NAligner/matrices/BLOSUM62
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 1eacd14..0000000
--- a/src/NAligner/matrices/BLOSUM65
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 3e4093f..0000000
--- a/src/NAligner/matrices/BLOSUM70
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 98964be..0000000
--- a/src/NAligner/matrices/BLOSUM75
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 78172a3..0000000
--- a/src/NAligner/matrices/BLOSUM80
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index cb47fd2..0000000
--- a/src/NAligner/matrices/BLOSUM85
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index 71441b5..0000000
--- a/src/NAligner/matrices/BLOSUM90
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index df064c8..0000000
--- a/src/NAligner/matrices/BLOSUMN
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
deleted file mode 100644
index e287ed0..0000000
--- a/src/NAligner/matrices/DAYHOFF
+++ /dev/null
@@ -1,32 +0,0 @@
-#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
deleted file mode 100644
index bfec6d9..0000000
--- a/src/NAligner/matrices/EDNAFULL
+++ /dev/null
@@ -1,25 +0,0 @@
-#
-# 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
deleted file mode 100644
index d7bd4f4..0000000
--- a/src/NAligner/matrices/GONNET
+++ /dev/null
@@ -1,26 +0,0 @@
-# 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
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-* -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
deleted file mode 100644
index 63913d5..0000000
--- a/src/NAligner/matrices/IDENTITY
+++ /dev/null
@@ -1,25 +0,0 @@
- A R N B D C Q Z E G H I L K M F P S T W Y V X *
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-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
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-* -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
deleted file mode 100644
index cda9e49..0000000
--- a/src/NAligner/matrices/MATCH
+++ /dev/null
@@ -1,25 +0,0 @@
- 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
deleted file mode 100644
index c164b06..0000000
--- a/src/NAligner/matrices/PAM10
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 2e33dd3..0000000
--- a/src/NAligner/matrices/PAM100
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 25b2c01..0000000
--- a/src/NAligner/matrices/PAM110
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 3cbb04b..0000000
--- a/src/NAligner/matrices/PAM120
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 0b47a5d..0000000
--- a/src/NAligner/matrices/PAM130
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 022c61b..0000000
--- a/src/NAligner/matrices/PAM140
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index c010eef..0000000
--- a/src/NAligner/matrices/PAM150
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index f30d717..0000000
--- a/src/NAligner/matrices/PAM160
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index ca090d6..0000000
--- a/src/NAligner/matrices/PAM170
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 84addeb..0000000
--- a/src/NAligner/matrices/PAM180
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 6840cc4..0000000
--- a/src/NAligner/matrices/PAM190
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 58cc98c..0000000
--- a/src/NAligner/matrices/PAM20
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index d4edff2..0000000
--- a/src/NAligner/matrices/PAM200
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 0b49af5..0000000
--- a/src/NAligner/matrices/PAM210
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 0834a92..0000000
--- a/src/NAligner/matrices/PAM220
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index c9ff6db..0000000
--- a/src/NAligner/matrices/PAM230
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index c17cdf8..0000000
--- a/src/NAligner/matrices/PAM240
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 17e9e60..0000000
--- a/src/NAligner/matrices/PAM250
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 5098eb4..0000000
--- a/src/NAligner/matrices/PAM260
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 322fcdb..0000000
--- a/src/NAligner/matrices/PAM270
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 2b09bca..0000000
--- a/src/NAligner/matrices/PAM280
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 6852c6a..0000000
--- a/src/NAligner/matrices/PAM290
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 8a01c88..0000000
--- a/src/NAligner/matrices/PAM30
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 5d1a5a8..0000000
--- a/src/NAligner/matrices/PAM300
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index cd0e5b0..0000000
--- a/src/NAligner/matrices/PAM310
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index d7fbbd2..0000000
--- a/src/NAligner/matrices/PAM320
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 77db35e..0000000
--- a/src/NAligner/matrices/PAM330
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 02c8540..0000000
--- a/src/NAligner/matrices/PAM340
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 140a6f2..0000000
--- a/src/NAligner/matrices/PAM350
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 5f6cd46..0000000
--- a/src/NAligner/matrices/PAM360
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index f72261f..0000000
--- a/src/NAligner/matrices/PAM370
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index cbcf063..0000000
--- a/src/NAligner/matrices/PAM380
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 8206530..0000000
--- a/src/NAligner/matrices/PAM390
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index e0df4f6..0000000
--- a/src/NAligner/matrices/PAM40
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 4d99c84..0000000
--- a/src/NAligner/matrices/PAM400
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index b7c9bfd..0000000
--- a/src/NAligner/matrices/PAM410
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 53e0caf..0000000
--- a/src/NAligner/matrices/PAM420
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 2450215..0000000
--- a/src/NAligner/matrices/PAM430
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 0429e87..0000000
--- a/src/NAligner/matrices/PAM440
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 30cc7a2..0000000
--- a/src/NAligner/matrices/PAM450
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 7491d6c..0000000
--- a/src/NAligner/matrices/PAM460
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 9d5e333..0000000
--- a/src/NAligner/matrices/PAM470
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index c777c62..0000000
--- a/src/NAligner/matrices/PAM480
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 107a0c8..0000000
--- a/src/NAligner/matrices/PAM490
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 6d37d4b..0000000
--- a/src/NAligner/matrices/PAM50
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 617c3f1..0000000
--- a/src/NAligner/matrices/PAM500
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index fba70b9..0000000
--- a/src/NAligner/matrices/PAM60
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index b20cdf0..0000000
--- a/src/NAligner/matrices/PAM70
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 55aa043..0000000
--- a/src/NAligner/matrices/PAM80
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index fa2d5b3..0000000
--- a/src/NAligner/matrices/PAM90
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# 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
deleted file mode 100644
index 8b5954e..0000000
--- a/src/NAligner/matrices/TEST1
+++ /dev/null
@@ -1,25 +0,0 @@
- 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
deleted file mode 100644
index 6a226c2..0000000
--- a/src/NAligner/naligner.sln
+++ /dev/null
@@ -1,21 +0,0 @@
-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
deleted file mode 100644
index fdc7ab7..0000000
--- a/src/NAligner/util/AlphanumericComparator.cs
+++ /dev/null
@@ -1,71 +0,0 @@
-#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
deleted file mode 100644
index f17d67f..0000000
--- a/src/NAligner/util/Commons.cs
+++ /dev/null
@@ -1,115 +0,0 @@
-#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
deleted file mode 100644
index d74c9d0..0000000
--- a/src/NAligner/util/NAlignerException.cs
+++ /dev/null
@@ -1,38 +0,0 @@
-#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
deleted file mode 100644
index 63a1181..0000000
--- a/src/NAligner/util/Tokenizer.cs
+++ /dev/null
@@ -1,195 +0,0 @@
-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
index 7592331..dba1fd3 100644
--- a/src/jaligner/Alignment.java
+++ b/src/jaligner/Alignment.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -26,10 +24,10 @@ import java.text.DecimalFormat;
/**
* Holds the output of a pairwise sequences alignment.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
-public class Alignment {
+public final class Alignment {
/**
* Gap character
@@ -39,12 +37,12 @@ public class Alignment {
/**
* Default name for sequence #1
*/
- private static final String DEFAULT_SEQUENCE1_NAME = "jaligner_1";
+ private static final String SEQUENCE1 = "jaligner_1";
/**
* Default name for sequence #2
*/
- private static final String DEFAULT_SEQUENCE2_NAME = "jaligner_2";
+ private static final String SEQUENCE2 = "jaligner_2";
/**
* Scoring matrix
@@ -116,6 +114,10 @@ public class Alignment {
*/
private int gaps;
+ private Sequence originalSequence1;
+
+ private Sequence originalSequence2;
+
/**
* Constructor for Alignment
*/
@@ -158,8 +160,7 @@ public class Alignment {
* @return Returns the name1.
*/
public String getName1() {
- return name1 == null || name1.length() == 0 ? DEFAULT_SEQUENCE1_NAME
- : name1;
+ return name1 == null || name1.trim().length() == 0 ? SEQUENCE1 : name1;
}
/**
@@ -174,8 +175,7 @@ public class Alignment {
* @return Returns the name2.
*/
public String getName2() {
- return name2 == null || name2.length() == 0 ? DEFAULT_SEQUENCE2_NAME
- : name2;
+ return name2 == null || name2.trim().length() == 0 ? SEQUENCE2 : name2;
}
/**
@@ -217,6 +217,15 @@ public class Alignment {
}
/**
+ * Returns the length of the alignment
+ *
+ * @return Alignment length
+ */
+ public int getLength() {
+ return this.sequence1.length;
+ }
+
+ /**
* @return Returns the sequence1.
*/
public char[] getSequence1() {
@@ -339,7 +348,7 @@ public class Alignment {
/**
* Returns a summary for alignment
*
- * @return alignment summary
+ * @return {@link String} alignment summary
*/
public String getSummary() {
StringBuffer buffer = new StringBuffer();
@@ -352,9 +361,9 @@ public class Alignment {
buffer.append(Commons.getLineSeparator());
buffer.append("Sequence #2: " + getName2());
buffer.append(Commons.getLineSeparator());
- buffer.append("Length #1: " + sequence1.length);
+ buffer.append("Length #1: " + getOriginalSequence1().length());
buffer.append(Commons.getLineSeparator());
- buffer.append("Length #2: " + sequence2.length);
+ buffer.append("Length #2: " + getOriginalSequence2().length());
buffer.append(Commons.getLineSeparator());
buffer.append("Matrix: "
+ (matrix.getId() == null ? "" : matrix.getId()));
@@ -382,19 +391,96 @@ public class Alignment {
/**
* Calculate the score of the alignment, not using the score field (the
- * function only uses sequence1, sequence2, matrix and gap penalties). (By:
- * Bram Minnaert)
+ * function only uses sequence1, sequence2, matrix and gap penalties).
*
- * @return the calculated score
+ * @return the calculated score (By: Bram Minnaert)
*/
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
+ // The calculated score
+ float calcScore = 0;
+
+ // In the previous step there was a gap in the first sequence
+ boolean previous1wasGap = false;
+
+ // In the previous step there was a gap in the second sequence
+ boolean previous2wasGap = false;
+
+ int start = 0;
+ int end = sequence1.length - 1;
+
char c1, c2; // the next character
- for (int i = 0, n = sequence1.length; i < n; i++) {
+ for (int i = start; i <= end; 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;
+ }
+
+ /**
+ * Calculate the score of the alignment without the terminal gaps.
+ *
+ */
+ public float getScoreWithNoTerminalGaps() {
+ // The calculated score
+ float calcScore = 0;
+
+ // In the previous step there was a gap in the first sequence
+ boolean previous1wasGap = false;
+
+ // In the previous step there was a gap in the second sequence
+ boolean previous2wasGap = false;
+
+ int start = 0;
+ int end = sequence1.length - 1;
+
+ if (sequence1[start] == GAP) {
+ while (sequence1[start] == GAP) {
+ start++;
+ }
+ } else if (sequence2[start] == GAP) {
+ while (sequence2[start] == GAP) {
+ start++;
+ }
+ }
+
+ if (sequence1[end] == GAP) {
+ while (sequence1[end] == GAP) {
+ end--;
+ }
+ } else if (sequence2[end] == GAP) {
+ while (sequence2[end] == GAP) {
+ end--;
+ }
+ }
+
+ char c1, c2; // the next character
+ for (int i = start; i <= end; i++) {
c1 = sequence1[i];
c2 = sequence2[i];
// the next character in the first sequence is a gap
@@ -439,4 +525,166 @@ public class Alignment {
return false;
}
}
+
+ /**
+ * Returns original {@link Sequence} #1
+ *
+ * @return original {@link Sequence} #1
+ */
+ public Sequence getOriginalSequence1() {
+ return originalSequence1;
+ }
+
+ /**
+ *
+ * @param originalSequence1
+ */
+ public void setOriginalSequence1(Sequence originalSequence1) {
+ this.originalSequence1 = originalSequence1;
+ }
+
+ /**
+ * Returns original {@link Sequence} #2
+ *
+ * @return original {@link Sequence} #2
+ */
+ public Sequence getOriginalSequence2() {
+ return originalSequence2;
+ }
+
+ /**
+ *
+ * @param originalSequence2
+ */
+ public void setOriginalSequence2(Sequence originalSequence2) {
+ this.originalSequence2 = originalSequence2;
+ }
+
+ /**
+ * Returns the number of gaps of the aligned sequence #1
+ *
+ * @return the number of gaps of the aligned sequence #1
+ */
+ public int getGaps1() {
+ int count = 0;
+ for (int i = 0, n = sequence1.length; i < n; i++) {
+ if (sequence1[i] == Alignment.GAP) {
+ count++;
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Returns the number of gaps of the aligned sequence #2
+ *
+ * @return the number of gaps of the aligned sequence #2
+ */
+ public int getGaps2() {
+ int count = 0;
+ for (int i = 0, n = sequence2.length; i < n; i++) {
+ if (sequence2[i] == Alignment.GAP) {
+ count++;
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Adds this alignment to another alignment, the order is important.
+ *
+ * @param a1
+ * The 1st alignment
+ * @param a2
+ * The 2nd alignment
+ * @return the sum of two alignment
+ */
+ public static Alignment add(Alignment a1, Alignment a2) {
+
+ if (a1 == null) {
+ if (a2 == null) {
+ return null;
+ } else {
+ return copy(a2);
+ }
+ } else {
+ if (a2 == null) {
+ return copy(a1);
+ } else {
+ Alignment sum = new Alignment();
+
+ StringBuffer buffer = new StringBuffer();
+
+ buffer.append(a1.getOriginalSequence1());
+ buffer.append(a2.getOriginalSequence1());
+
+ sum.setOriginalSequence1(new Sequence(buffer.toString()));
+
+ buffer = new StringBuffer();
+
+ buffer.append(a1.getOriginalSequence2());
+ buffer.append(a2.getOriginalSequence2());
+
+ sum.setOriginalSequence2(new Sequence(buffer.toString()));
+
+ buffer = new StringBuffer();
+
+ buffer.append(a1.getSequence1());
+ buffer.append(a2.getSequence1());
+
+ sum.setSequence1(buffer.toString().toCharArray());
+
+ buffer = new StringBuffer();
+
+ buffer.append(a1.getSequence2());
+ buffer.append(a2.getSequence2());
+
+ sum.setSequence2(buffer.toString().toCharArray());
+
+ buffer = new StringBuffer();
+
+ buffer.append(a1.getMarkupLine());
+ buffer.append(a2.getMarkupLine());
+
+ sum.setMarkupLine(buffer.toString().toCharArray());
+
+ sum.setScore(a1.getScore() + a2.getScore());
+ sum.setGaps(a1.getGaps() + a2.getGaps());
+
+ sum.setStart1(a1.getStart1());
+ sum.setStart2(a1.getStart2());
+ sum.setExtend(a1.getExtend());
+ sum.setOpen(a1.getOpen());
+ sum.setMatrix(a1.getMatrix());
+
+ return sum;
+ }
+ }
+ }
+
+ /**
+ * Copies an alignment to another alignment.
+ *
+ * @param alignment
+ * Alignment
+ */
+ public static Alignment copy(Alignment alignment) {
+
+ Alignment copy = new Alignment();
+
+ copy.setSequence1(alignment.getSequence1());
+ copy.setSequence2(alignment.getSequence2());
+ copy.setMarkupLine(alignment.getMarkupLine());
+ copy.setScore(alignment.getScore());
+ copy.setGaps(alignment.getGaps());
+ copy.setStart1(alignment.getStart1());
+ copy.setStart2(alignment.getStart2());
+ copy.setExtend(alignment.getExtend());
+ copy.setOpen(alignment.getOpen());
+ copy.setMatrix(alignment.getMatrix());
+ copy.setOriginalSequence1(alignment.getOriginalSequence1());
+ copy.setOriginalSequence2(alignment.getOriginalSequence2());
+
+ return copy;
+ }
}
\ No newline at end of file
diff --git a/src/jaligner/Cell.java b/src/jaligner/Cell.java
index e452403..5e03ba9 100644
--- a/src/jaligner/Cell.java
+++ b/src/jaligner/Cell.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -21,7 +19,7 @@ package jaligner;
/**
* A cell in a similarity matrix, to hold row, column and score.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class Cell {
diff --git a/src/jaligner/Directions.java b/src/jaligner/Directions.java
index f876864..c17d1b5 100644
--- a/src/jaligner/Directions.java
+++ b/src/jaligner/Directions.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -21,7 +19,7 @@ package jaligner;
/**
* Traceback directions.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public abstract class Directions {
diff --git a/src/jaligner/Markups.java b/src/jaligner/Markups.java
index 4b3b342..722c503 100644
--- a/src/jaligner/Markups.java
+++ b/src/jaligner/Markups.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -21,7 +19,7 @@ package jaligner;
/**
* Markups line characters.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public abstract class Markups {
diff --git a/src/jaligner/NeedlemanWunsch.java b/src/jaligner/NeedlemanWunsch.java
new file mode 100644
index 0000000..646d2fc
--- /dev/null
+++ b/src/jaligner/NeedlemanWunsch.java
@@ -0,0 +1,302 @@
+/*
+ * 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;
+
+/**
+ * An implementation of the Needleman-Wunsch algorithm for biological global
+ * pairwise sequence alignment.
+ *
+ * <br>
+ * Reference: <a
+ * href="http://www.sbc.su.se/~per/molbioinfo2001/dynprog/adv_dynamic.html">Advanced
+ * Dynamic Programming Tutorial</a>.
+ *
+ *
+ * @author Ahmed Moustafa
+ */
+
+public final class NeedlemanWunsch {
+ /**
+ * Hidden constructor
+ */
+ private NeedlemanWunsch() {
+ super();
+ }
+
+ /**
+ * Aligns two sequences by Needleman-Wunsch (global)
+ *
+ * @param s1
+ * sequene #1 ({@link Sequence})
+ * @param s2
+ * sequene #2 ({@link Sequence})
+ * @param matrix
+ * scoring matrix ({@link Matrix})
+ * @param gap
+ * open 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 gap) {
+ float[][] scores = matrix.getScores();
+
+ int m = s1.length() + 1;
+ int n = s2.length() + 1;
+
+ byte[][] pointers = new byte[m][n];
+
+ // Initializes the element (0,0) of the traceback matrix to STOP.
+ pointers[0][0] = Directions.STOP;
+
+ // Initializes the boundaries of the traceback matrix.
+ for (int i = 1; i < m; i++) {
+ pointers[i][0] = Directions.UP;
+ }
+ for (int j = 1; j < n; j++) {
+ pointers[0][j] = Directions.LEFT;
+ }
+
+ Cell cell = construct(s1, s2, scores, gap, pointers);
+ Alignment alignment = traceback(s1, s2, matrix, pointers, cell);
+
+ alignment.setOriginalSequence1(s1);
+ alignment.setOriginalSequence2(s2);
+ alignment.setMatrix(matrix);
+ alignment.setOpen(gap);
+ alignment.setExtend(gap);
+
+ if (s1.getId() != null) {
+ alignment.setName1(s1.getId());
+ }
+ if (s2.getId() != null) {
+ alignment.setName2(s2.getId());
+ }
+
+ return alignment;
+ }
+
+ /**
+ * Constructs directions matrix for the traceback.
+ *
+ * @param s1
+ * sequence #1
+ * @param s2
+ * sequence #2
+ * @param matrix
+ * scoring matrix
+ * @param gap
+ * gap penalty
+ * @param pointers
+ * traceback matrix
+ *
+ * @return The cell where the traceback starts.
+ */
+ private static Cell construct(Sequence s1, Sequence s2, float[][] matrix,
+ float gap, byte[][] pointers) {
+
+ Cell cell = new Cell();
+
+ char[] a1 = s1.toArray();
+ char[] a2 = s2.toArray();
+
+ int m = s1.length() + 1; // number of rows in similarity matrix
+ int n = s2.length() + 1; // number of columns in similarity matrix
+
+ // float[] v = new float[n]; // optimal alignment
+ float[] v = new float[n];
+
+ // Initialization of v
+ for (int j = 1; j < n; j++) {
+ v[j] = j * -gap;
+ }
+ v[0] = 0;
+
+ float x, y, z;
+ float vOld = 0;
+
+ // Fill the matrices
+ for (int i = 1; i < m; i++) { // for all rows
+ v[0] = i * -gap;
+
+ for (int j = 1; j < n; j++) { // for all columns
+
+ x = v[j] - gap;
+ y = v[j - 1] - gap;
+ z = vOld + matrix[a1[i - 1]][a2[j - 1]];
+
+ vOld = v[j];
+ v[j] = maximum(x, y, z);
+
+ // Determine the traceback direction
+ if (v[j] == x) {
+ pointers[i][j] = Directions.UP;
+ } else if (v[j] == y) {
+ pointers[i][j] = Directions.LEFT;
+ } else {
+ pointers[i][j] = Directions.DIAGONAL;
+ }
+
+ } // loop columns
+
+ vOld = i * -gap;
+ } // loop rows
+
+ // cell contains the row number, the column number
+ // and the score of the cell with the maximum score
+
+ // Set the traceback start at the last cell m, n
+ // because we are doing global alignment
+ cell.set(m - 1, n - 1, v[n - 1]);
+ 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 pointers
+ * traceback 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 static Alignment traceback(Sequence s1, Sequence s2, Matrix m,
+ byte[][] pointers, Cell cell) {
+ char[] array1 = s1.toArray();
+ char[] array2 = s2.toArray();
+ float[][] scores = m.getScores();
+
+ Alignment alignment = new Alignment();
+ alignment.setScore(cell.getScore());
+
+ // maximum length after the aligned sequences
+ int maxlen = s1.length() + s2.length();
+
+ 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
+
+ // Traceback flag, where true => continue and false => stop
+ boolean stillGoing = true;
+ while (stillGoing) {
+ switch (pointers[i][j]) {
+ case Directions.UP:
+ reversed1[len1++] = array1[--i];
+ reversed2[len2++] = Alignment.GAP;
+ reversed3[len3++] = Markups.GAP;
+ gaps++;
+ break;
+ case Directions.DIAGONAL:
+ c1 = array1[--i];
+ c2 = array2[--j];
+ 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:
+ reversed1[len1++] = Alignment.GAP;
+ reversed2[len2++] = array2[--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);
+
+ return alignment;
+ }
+
+ /**
+ * Returns the maximum of two float numbers.
+ *
+ * @param a
+ * float #1
+ * @param b
+ * float #2
+ * @param c
+ * float #3
+ * @return the maximum of a and b
+ */
+ private static float maximum(float a, float b, float c) {
+ if (a > b) {
+ return a > c ? a : c;
+ } else {
+ return b > c ? b : c;
+ }
+ }
+
+ /**
+ * 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/NeedlemanWunschGotoh.java b/src/jaligner/NeedlemanWunschGotoh.java
new file mode 100644
index 0000000..6088630
--- /dev/null
+++ b/src/jaligner/NeedlemanWunschGotoh.java
@@ -0,0 +1,427 @@
+/*
+ * 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 Needleman-Wunsch algorithm with Gotoh's improvement
+ * for biological global pairwise sequence alignment.
+ *
+ * @author Ahmed Moustafa
+ * @author Bram Minnaert
+ */
+
+public final class NeedlemanWunschGotoh {
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger
+ .getLogger(NeedlemanWunschGotoh.class.getSimpleName());
+
+ /**
+ * Hidden constructor
+ */
+ private NeedlemanWunschGotoh() {
+ super();
+ }
+
+ /**
+ * Aligns two sequences by Needleman-Wunsch (global)
+ *
+ * @param s1
+ * sequene #1 ({@link Read})
+ * @param s2
+ * sequene #2 ({@link Read})
+ * @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 Read
+ * @see Matrix
+ */
+ public static Alignment align(Sequence s1, Sequence s2, Matrix matrix,
+ float o, float e) {
+
+ float[][] scores = matrix.getScores();
+
+ Sequence _s1;
+ Sequence _s2;
+
+ if (s1.length() < s2.length()) {
+ _s1 = s2;
+ _s2 = s1;
+ } else {
+ _s1 = s1;
+ _s2 = s2;
+ }
+
+ int m = _s1.length() + 1;
+ int n = _s2.length() + 1;
+
+ byte[] pointers = new byte[m * n];
+
+ int[] lengths = new int[m * n];
+
+ // Initializes the element (0,0) of the traceback matrix to STOP.
+ pointers[0] = Directions.STOP;
+
+ // Initializes the boundaries of the traceback matrix.
+ for (int i = 1, k = n; i < m; i++, k += n) {
+ pointers[k] = Directions.UP;
+ lengths[k] = i;
+ }
+ for (int j = 1; j < n; j++) {
+ pointers[j] = Directions.LEFT;
+ lengths[j] = j;
+ }
+
+ Cell cell = construct(_s1, _s2, scores, o, e, pointers, lengths);
+
+ Alignment alignment = traceback(_s1, _s2, matrix, pointers, cell,
+ lengths);
+
+ alignment.setMatrix(matrix);
+ alignment.setOpen(o);
+ alignment.setExtend(e);
+ alignment.setName1(_s1.getId());
+ alignment.setName2(_s2.getId());
+ alignment.setOriginalSequence1(_s1);
+ alignment.setOriginalSequence2(_s2);
+
+ 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
+ * @param pointers
+ * traceback matrix
+ *
+ * @return The cell where the traceback starts.
+ */
+ private static Cell construct(Sequence s1, Sequence s2, float[][] matrix,
+ float o, float e, byte[] pointers, int[] lengths) {
+
+ logger.info("Started...");
+
+ char[] a1 = s1.toArray();
+ char[] a2 = s2.toArray();
+
+ int m = s1.length() + 1; // number of rows in similarity matrix
+ int n = s2.length() + 1; // number of columns in similarity matrix
+
+ float[] v = new float[n];
+ float vDiagonal = 0;// Float.NEGATIVE_INFINITY; // best score in cell
+ float f = Float.NEGATIVE_INFINITY; // score from diagonal
+ float h = Float.NEGATIVE_INFINITY; // best score ending with gap from
+ // left
+ float[] g = new float[n]; // best score ending with gap from above
+
+ // Initialization of v and g
+ g[0] = Float.NEGATIVE_INFINITY;
+ for (int j = 1; j < n; j++) {
+ v[j] = 0;// -o - (j - 1) * e;
+ g[j] = Float.NEGATIVE_INFINITY;
+ }
+
+ int lengthOfHorizontalGap = 0;
+ int[] lengthOfVerticalGap = new int[n];
+
+ float similarityScore;
+ float maximumScore = Float.NEGATIVE_INFINITY;
+ int maxi = 0;
+ int maxj = 0;
+
+ // Fill the matrices
+ for (int i = 1, k = n; i < m; i++, k += n) { // for all rows
+ v[0] = -o - (i - 1) * e;
+ for (int j = 1, l = k + 1; j < n; j++, l++) { // for all columns
+
+ similarityScore = matrix[a1[i - 1]][a2[j - 1]];
+
+ f = vDiagonal + similarityScore;// from diagonal
+
+ // Which cell from the left?
+ if (h - e >= v[j - 1] - o) {
+ h -= e;
+ lengthOfHorizontalGap++;
+ } else {
+ h = v[j - 1] - o;
+ lengthOfHorizontalGap = 1;
+ }
+
+ // Which cell from above?
+ if (g[j] - e >= v[j] - o) {
+ g[j] = g[j] - e;
+ lengthOfVerticalGap[j] = lengthOfVerticalGap[j] + 1;
+ } else {
+ g[j] = v[j] - o;
+ lengthOfVerticalGap[j] = 1;
+ }
+
+ vDiagonal = v[j];
+ v[j] = maximum(f, g[j], h); // best one
+ if (v[j] > maximumScore) {
+ maximumScore = v[j];
+ maxi = i;
+ maxj = j;
+ }
+
+ // Determine the traceback direction
+ if (v[j] == f) {
+ pointers[l] = Directions.DIAGONAL;
+ } else if (v[j] == g[j]) {
+ pointers[l] = Directions.UP;
+ lengths[l] = lengthOfVerticalGap[j];
+ } else if (v[j] == h) {
+ pointers[l] = Directions.LEFT;
+ lengths[l] = lengthOfHorizontalGap;
+ }
+
+ } // loop columns
+
+ // Reset
+ h = Float.NEGATIVE_INFINITY;
+ vDiagonal = 0;// -o - (i - 1) * e;
+
+ lengthOfHorizontalGap = 0;
+
+ } // loop rows
+
+ Cell cell = new Cell();
+ cell.set(maxi, maxj, v[n - 1]);
+
+ logger.info("Finished.");
+
+ 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 pointers
+ * traceback 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 static Alignment traceback(Sequence s1, Sequence s2, Matrix m,
+ byte[] pointers, Cell cell, int[] lengths) {
+ logger.info("Started...");
+
+ char[] array1 = s1.toArray();
+ char[] array2 = s2.toArray();
+ float[][] scores = m.getScores();
+
+ Alignment alignment = new Alignment();
+ alignment.setScore(cell.getScore());
+
+ // maximum length after the aligned sequences
+ int maxlen = s1.length() + s2.length();
+
+ 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 n = s2.length() + 1;
+ int row = i * n;
+
+ int a = s1.length() - 1;
+ int b = s2.length() - 1;
+ if (a - i > b - j) {
+ for (; a - i > b - j; a--) {
+ reversed1[len1++] = array1[a];
+ reversed2[len2++] = Alignment.GAP;
+ reversed3[len3++] = Markups.GAP;
+ gaps++;
+ }
+ for (; b > j - 1; a--, b--) {
+ c1 = array1[a];
+ c2 = array2[b];
+
+ 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;
+ }
+ }
+ } else {
+ for (; b - j > a - i; b--) {
+ reversed1[len1++] = Alignment.GAP;
+ reversed2[len2++] = array2[b];
+ reversed3[len3++] = Markups.GAP;
+ gaps++;
+ }
+ for (; a > i - 1; a--, b--) {
+ c1 = array1[a];
+ c2 = array2[b];
+
+ 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;
+ }
+ }
+ }
+
+ // Traceback flag, where true => continue and false => stop
+ boolean stillGoing = true;
+ while (stillGoing) {
+ int l = row + j;
+ switch (pointers[l]) {
+ case Directions.UP:
+ for (int k = 0, len = lengths[l]; k < len; k++) {
+ reversed1[len1++] = array1[--i];
+ reversed2[len2++] = Alignment.GAP;
+ reversed3[len3++] = Markups.GAP;
+ row -= n;
+ gaps++;
+ }
+ break;
+ case Directions.DIAGONAL:
+ c1 = array1[--i];
+ c2 = array2[--j];
+ reversed1[len1++] = c1;
+ reversed2[len2++] = c2;
+ row -= n;
+ 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 k = 0, len = lengths[l]; k < len; k++) {
+ reversed1[len1++] = Alignment.GAP;
+ reversed2[len2++] = array2[--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.");
+
+ return alignment;
+ }
+
+ /**
+ * Returns the maximum of two float numbers.
+ *
+ * @param a
+ * float #1
+ * @param b
+ * float #2
+ * @param c
+ * float #3
+ * @return the maximum of a and b
+ */
+ private static float maximum(float a, float b, float c) {
+ if (a > b) {
+ return a > c ? a : c;
+ } else {
+ return b > c ? b : c;
+ }
+ }
+
+ /**
+ * 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/Sequence.java b/src/jaligner/Sequence.java
index 2d6e823..431a6d8 100644
--- a/src/jaligner/Sequence.java
+++ b/src/jaligner/Sequence.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -15,38 +13,41 @@
* 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.util.Commons;
+
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)
+ * A basic (nucleic or protein) sequence. It's a wrapper to
+ * {@link java.lang.String}.
+ *
+ * @author Ahmed Moustafa
*/
public class Sequence implements Serializable {
/**
- *
- */
- private static final long serialVersionUID = 3256721801357898297L;
+ *
+ */
+ private static final long serialVersionUID = 3256721801357898297L;
- /**
+ /**
* Sequence type nucleic.
*/
- public static final int NUCLEIC = 0;
-
- /**
- * Sequence type protein.
- */
+ public static final int NUCLEIC = 0;
+
+ /**
+ * Sequence type protein.
+ */
public static final int PROTEIN = 1;
-
+
/**
* Sequence
*/
private String sequence;
-
+
/**
* Sequence id.
*/
@@ -56,140 +57,193 @@ public class Sequence implements Serializable {
* Sequence description.
*/
private String description = null;
-
+
/**
* Sequence type.
*/
private int type = PROTEIN;
-
+
/**
* Constructor
*/
- public Sequence( ) {
- super();
+ public Sequence() {
+ super();
}
/**
* Constructor
+ *
* @param sequence
*/
public Sequence(String sequence) {
- super();
- this.sequence = sequence;
+ super();
+ this.sequence = sequence;
}
-
/**
* Constructor
+ *
+ * @param name
+ * @param sequence
+ */
+ public Sequence(String name, char[] sequence) {
+ super();
+ this.id = name;
+ this.sequence = new String(sequence);
+ }
+
+ /**
+ * Constructor
+ *
+ * @param name
+ * @param sequence
+ */
+ public Sequence(String name, String sequence) {
+ super();
+ this.id = name;
+ 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;
+ 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 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 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
+ *
+ * @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 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();
+ }
/**
- * Returns the sequence as an array of characters.
- * @return array of chars.
+ * Returns the sequence id and the sequence string
+ *
+ * @return sequence id and the sequence string
*/
- public char[] toArray( ) {
- return this.sequence.toCharArray();
+ @Override
+ public String toString() {
+ return id + Commons.TAB + sequence;
}
}
\ No newline at end of file
diff --git a/src/jaligner/SmithWatermanGotoh.java b/src/jaligner/SmithWatermanGotoh.java
index 7e48bdb..56b6719 100644
--- a/src/jaligner/SmithWatermanGotoh.java
+++ b/src/jaligner/SmithWatermanGotoh.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -26,10 +24,30 @@ 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)
+ * <strong>Recursive definition:</strong>
+ * <ul>
+ * <li>
+ * <strong>Base conditions:</strong>
+ * <ul>
+ * <li><code>V(0, 0) = 0</code></li>
+ * <li><code>V(i, 0) = E(i, 0) = W<sub>g</sub> + iW<sub>s</sub></code></li>
+ * <li><code>V(0, j) = F(0, j) = W<sub>g</sub> + jW<sub>s</sub></code></li>
+ * </ul>
+ * </li>
+ * <li>
+ * <strong>Recurrence relation:</strong>
+ * <ul>
+ * <li><code>V(i, j) = max{E(i, j), F(i, j), G(i, j)}</code>, where:</li>
+ * <li><code>G(i, j) = V(i - 1, j - 1) + similarity(S<sub>i</sub>, T<sub>j</sub>)</code></li>
+ * <li><code>E(i, j) = max{E(i, j - 1) + W<sub>s</sub>, V(i, j - 1) + W<sub>g</sub> + W<sub>s</sub>}</code></li>
+ * <li><code>F(i, j) = max{F(i - 1, j) + W<sub>s</sub>, V(i - 1, j) + W<sub>g</sub> + W<sub>s</sub>}</code></li>
+ * </ul>
+ * </ul>
+ *
+ * @author Ahmed Moustafa
*/
-public class SmithWatermanGotoh {
+public final class SmithWatermanGotoh {
/**
* Hidden constructor
*/
@@ -44,7 +62,7 @@ public class SmithWatermanGotoh {
.getLogger(SmithWatermanGotoh.class.getName());
/**
- * Aligns two sequences by Smith-Waterman algorithm
+ * Aligns two sequences by Smith-Waterman (local)
*
* @param s1
* sequene #1 ({@link Sequence})
@@ -67,8 +85,6 @@ public class SmithWatermanGotoh {
long start = System.currentTimeMillis();
float[][] scores = matrix.getScores();
- SmithWatermanGotoh sw = new SmithWatermanGotoh();
-
int m = s1.length() + 1;
int n = s2.length() + 1;
@@ -90,17 +106,23 @@ public class SmithWatermanGotoh {
}
}
- 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());
+ Cell cell = SmithWatermanGotoh.construct(s1, s2, scores, o, e,
+ pointers, sizesOfVerticalGaps, sizesOfHorizontalGaps);
+ Alignment alignment = SmithWatermanGotoh.traceback(s1, s2, matrix,
+ pointers, cell, sizesOfVerticalGaps, sizesOfHorizontalGaps);
+ alignment.setOriginalSequence1(s1);
+ alignment.setOriginalSequence2(s2);
alignment.setMatrix(matrix);
alignment.setOpen(o);
alignment.setExtend(e);
- logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");
+ if (s1.getId() != null) {
+ alignment.setName1(s1.getId());
+ }
+ if (s2.getId() != null) {
+ alignment.setName2(s2.getId());
+ }
+ String msg = "Finished in " + (System.currentTimeMillis() - start) + " milliseconds";
+ logger.info(msg);
return alignment;
}
@@ -119,12 +141,12 @@ public class SmithWatermanGotoh {
* 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,
+ private static 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();
@@ -134,7 +156,8 @@ public class SmithWatermanGotoh {
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[] v = new float[n]; // best score of alignment x1...xi to
+ // y1...yi
float vDiagonal;
g[0] = Float.NEGATIVE_INFINITY;
@@ -197,8 +220,8 @@ public class SmithWatermanGotoh {
}
}
}
- logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");
+ String msg = "Finished in " + (System.currentTimeMillis() - start) + " milliseconds";
+ logger.info(msg);
return cell;
}
@@ -219,15 +242,15 @@ public class SmithWatermanGotoh {
* @see Cell
* @see Alignment
*/
- private Alignment traceback(Sequence s1, Sequence s2, Matrix m,
+ private static 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;
@@ -236,7 +259,7 @@ public class SmithWatermanGotoh {
alignment.setScore(cell.getScore());
int maxlen = s1.length() + s2.length(); // maximum length after the
- // aligned sequences
+ // aligned sequences
char[] reversed1 = new char[maxlen]; // reversed sequence #1
char[] reversed2 = new char[maxlen]; // reversed sequence #2
@@ -257,7 +280,7 @@ public class SmithWatermanGotoh {
int k = i * n;
boolean stillGoing = true; // traceback flag: true -> continue & false
- // -> stop
+ // -> stop
while (stillGoing) {
switch (pointers[k + j]) {
@@ -309,8 +332,8 @@ public class SmithWatermanGotoh {
alignment.setGaps(gaps);
alignment.setSimilarity(similarity);
- logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");
+ String msg = "Finished in " + (System.currentTimeMillis() - start) + " milliseconds";
+ logger.info(msg);
return alignment;
}
diff --git a/src/jaligner/TracebackNode.java b/src/jaligner/TracebackNode.java
new file mode 100644
index 0000000..19de1ab
--- /dev/null
+++ b/src/jaligner/TracebackNode.java
@@ -0,0 +1,97 @@
+/*
+ * 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 node
+ *
+ * @author Bram Minnaert
+ * @author Ahmed Moustafa
+ */
+
+public final class TracebackNode {
+
+ /**
+ * Direction
+ */
+ private byte direction;
+
+ /**
+ * Length of gap (for up and left directions)
+ */
+ private int length;
+
+ /**
+ * Constructor
+ */
+ public TracebackNode() {
+ super();
+ }
+
+ /**
+ * Sets the direction to diagonal
+ *
+ */
+ public void setDiagonal() {
+ direction = Directions.DIAGONAL;
+ length = 0;
+ }
+
+ /**
+ * Sets the direction to up
+ *
+ * @param length
+ * length of gap
+ */
+ public void setUp(int length) {
+ direction = Directions.UP;
+ this.length = length;
+ }
+
+ /**
+ * Sets the direction to left
+ *
+ * @param length
+ * length of gap
+ */
+ public void setLeft(int length) {
+ direction = Directions.LEFT;
+ this.length = length;
+ }
+
+ /**
+ * Sets the direction to stop
+ */
+ public void setStop() {
+ direction = Directions.STOP;
+ length = 0;
+ }
+
+ /**
+ * @return Returns the direction.
+ */
+ public byte getDirection() {
+ return direction;
+ }
+
+ /**
+ * @return Returns the length.
+ */
+ public int getLength() {
+ return length;
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/example/NeedlemanWunschExample.java b/src/jaligner/example/NeedlemanWunschExample.java
new file mode 100644
index 0000000..89f841c
--- /dev/null
+++ b/src/jaligner/example/NeedlemanWunschExample.java
@@ -0,0 +1,72 @@
+/*
+ * 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.NeedlemanWunsch;
+import jaligner.Sequence;
+import jaligner.formats.Pair;
+import jaligner.matrix.Matrix;
+import jaligner.matrix.MatrixGenerator;
+import jaligner.util.SequenceParser;
+
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Example of using JAligner API to perform global pairwise sequence alignment
+ * with Needleman-Wunsch algorithm {@link jaligner.NeedlemanWunsch}.
+ *
+ * @author Ahmed Moustafa
+ */
+
+public class NeedlemanWunschExample {
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger
+ .getLogger(NeedlemanWunschExample.class.getName());
+
+ /**
+ *
+ * @param args
+ */
+ public static void main(String[] args) {
+ try {
+ logger.info("Running example...");
+
+ Sequence s1 = SequenceParser.parse("GAATTCAGTTA");
+ Sequence s2 = SequenceParser.parse("GGATCGA");
+
+ float match = 2;
+ float mismatch = -1;
+ Matrix matrix = MatrixGenerator.generate(match, mismatch);
+ float gap = 2;
+
+ Alignment alignment = NeedlemanWunsch.align(s1, s2, matrix, gap);
+
+ 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);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/example/NeedlemanWunschGotohExample.java b/src/jaligner/example/NeedlemanWunschGotohExample.java
new file mode 100644
index 0000000..b0c59e0
--- /dev/null
+++ b/src/jaligner/example/NeedlemanWunschGotohExample.java
@@ -0,0 +1,91 @@
+/*
+ * $Id: NeedlemanWunschGotohExample.java,v 1.1 2006/02/03 05:00:23 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;
+/*
+ * 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.
+ */
+
+import jaligner.Alignment;
+import jaligner.NeedlemanWunschGotoh;
+import jaligner.Sequence;
+import jaligner.formats.Pair;
+import jaligner.matrix.Matrix;
+import jaligner.matrix.MatrixGenerator;
+import jaligner.util.SequenceParser;
+
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+/**
+ * Example of using JAligner API to perform global pairwise sequence alignment
+ * with {@link jaligner.NeedlemanWunschGotoh}.
+ *
+ * @author Ahmed Moustafa
+ */
+
+public class NeedlemanWunschGotohExample {
+
+ /**
+ * Logger
+ */
+ private static final Logger logger = Logger
+ .getLogger(NeedlemanWunschGotohExample.class.getName());
+
+ /**
+ *
+ * @param args
+ */
+ public static void main(String[] args) {
+ try {
+ logger.info("Running example...");
+
+ Sequence s1 = SequenceParser.parse("GAATTCAGTTA");
+ Sequence s2 = SequenceParser.parse("GGATCGA");
+
+ float match = 2;
+ float mismatch = -1;
+ Matrix matrix = MatrixGenerator.generate(match, mismatch);
+ float open = 2;
+ float extend = 2;
+
+ Alignment alignment = NeedlemanWunschGotoh.align(s1, s2, matrix,
+ open, extend);
+
+ 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);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/jaligner/example/Example.java b/src/jaligner/example/SmithWatermanGotohExample.java
similarity index 90%
rename from src/jaligner/example/Example.java
rename to src/jaligner/example/SmithWatermanGotohExample.java
index ab213c7..42a024a 100644
--- a/src/jaligner/example/Example.java
+++ b/src/jaligner/example/SmithWatermanGotohExample.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -34,10 +32,10 @@ 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)
+ * @author Ahmed Moustafa
*/
-public class Example {
+public class SmithWatermanGotohExample {
/**
*
@@ -52,7 +50,7 @@ public class Example {
/**
* Logger
*/
- private static final Logger logger = Logger.getLogger(Example.class.getName());
+ private static final Logger logger = Logger.getLogger(SmithWatermanGotohExample.class.getName());
/**
*
@@ -83,7 +81,7 @@ public class Example {
* @throws IOException
*/
private static String loadSampleSequence(String path) throws IOException {
- InputStream inputStream = Example.class.getClassLoader().getResourceAsStream(path);
+ InputStream inputStream = NeedlemanWunschExample.class.getClassLoader().getResourceAsStream(path);
StringBuffer buffer = new StringBuffer();
int ch;
while ((ch = inputStream.read()) != -1) {
diff --git a/src/jaligner/example/package.html b/src/jaligner/example/package.html
index c42043b..7ece5a1 100644
--- a/src/jaligner/example/package.html
+++ b/src/jaligner/example/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
Example for using API of JAligner to perform pairwise sequence alignment.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</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
index d5f776a..1591a95 100644
--- a/src/jaligner/example/sequences/p53_human.fasta
+++ b/src/jaligner/example/sequences/p53_human.fasta
@@ -1,7 +1,7 @@
->p53_human
-MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
-PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
-CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
-TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACAGR
-DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
+>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
index 65e7f3b..9b011cd 100644
--- a/src/jaligner/example/sequences/p53_mouse.fasta
+++ b/src/jaligner/example/sequences/p53_mouse.fasta
@@ -1,8 +1,8 @@
->p53_mouse
-MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEA
-LRVSGAPAAQDPVTETPGPAAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVM
-CTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCS
-DGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCM
-GGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGS
-AKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSR
+>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
index 5630321..8a85d59 100644
--- a/src/jaligner/formats/CLUSTAL.java
+++ b/src/jaligner/formats/CLUSTAL.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -44,7 +42,7 @@ import jaligner.Alignment;
* </small>
* </pre>
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class CLUSTAL extends Format {
diff --git a/src/jaligner/formats/FASTA.java b/src/jaligner/formats/FASTA.java
index 2a3b3f3..8b5ea61 100644
--- a/src/jaligner/formats/FASTA.java
+++ b/src/jaligner/formats/FASTA.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -24,7 +22,7 @@ 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)
+ * @author Ahmed Moustafa
*/
public class FASTA extends Format {
diff --git a/src/jaligner/formats/Format.java b/src/jaligner/formats/Format.java
index f59cdae..b36616e 100644
--- a/src/jaligner/formats/Format.java
+++ b/src/jaligner/formats/Format.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,7 +21,7 @@ import jaligner.Alignment;
/**
* Abstract format
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public abstract class Format {
diff --git a/src/jaligner/formats/FormatFactory.java b/src/jaligner/formats/FormatFactory.java
index ba884de..f4bac03 100644
--- a/src/jaligner/formats/FormatFactory.java
+++ b/src/jaligner/formats/FormatFactory.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -24,7 +22,7 @@ import java.util.HashMap;
/**
* Formats factory.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class FormatFactory {
@@ -36,7 +34,7 @@ public class FormatFactory {
/**
* {@link HashMap} of {@link Format}
*/
- private HashMap formats = new HashMap();
+ private HashMap<String, Format> formats = new HashMap<String, Format>();
/**
* Hidden constructor
@@ -78,7 +76,7 @@ public class FormatFactory {
* Returns a list of registered formats
* @return {@link Collection}
*/
- public Collection getFormats( ) {
+ public Collection<String> getFormats( ) {
return formats.keySet();
}
}
\ No newline at end of file
diff --git a/src/jaligner/formats/Pair.java b/src/jaligner/formats/Pair.java
index cf707bb..5d2449a 100644
--- a/src/jaligner/formats/Pair.java
+++ b/src/jaligner/formats/Pair.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -22,9 +20,9 @@ import jaligner.Alignment;
import jaligner.util.Commons;
/**
- * <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.
+ * <a href="http://emboss.sourceforge.net/docs/themes/AlignFormats.html">Alignment Formats</a>.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class Pair extends Format {
diff --git a/src/jaligner/formats/package.html b/src/jaligner/formats/package.html
index 5b3633b..8123e2c 100644
--- a/src/jaligner/formats/package.html
+++ b/src/jaligner/formats/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
Group of formats for output alignments.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/matrix/MatricesCompartor.java b/src/jaligner/matrix/MatricesCompartor.java
index 6aedcdd..82feec9 100644
--- a/src/jaligner/matrix/MatricesCompartor.java
+++ b/src/jaligner/matrix/MatricesCompartor.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,18 +21,15 @@ import java.util.Comparator;
/**
* Comparator to sort the scoring matrices by their names.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
-public class MatricesCompartor implements Comparator {
+public class MatricesCompartor implements Comparator<String> {
/* (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;
-
+ public int compare(String s1, String s2) {
int index1 = firstDigitIndex(s1);
int index2 = firstDigitIndex(s2);
diff --git a/src/jaligner/matrix/Matrix.java b/src/jaligner/matrix/Matrix.java
index 79ae0e3..68d24bd 100644
--- a/src/jaligner/matrix/Matrix.java
+++ b/src/jaligner/matrix/Matrix.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,51 +21,58 @@ import java.io.Serializable;
/**
* Scoring matrix.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class Matrix implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 3833742170619524400L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3833742170619524400L;
+
+ /**
+ * 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.
+ */
+ public static final int SIZE = 127;
+
+ /**
+ * Matrix id (or name)
+ */
+ private final String id;
+
+ /**
+ * Scores
+ */
+ private final float[][] scores;
+
+ 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;
+ }
- /**
- * 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];
- }
+ /**
+ *
+ * @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/MatrixGenerator.java b/src/jaligner/matrix/MatrixGenerator.java
new file mode 100644
index 0000000..0f73281
--- /dev/null
+++ b/src/jaligner/matrix/MatrixGenerator.java
@@ -0,0 +1,59 @@
+/*
+ * 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;
+
+/**
+ * A utility class to generate a scoring matrix from a fixed match and mismatch
+ * scoring scheme.
+ *
+ * @author Ahmed Moustafa
+ */
+
+public final class MatrixGenerator {
+
+ /**
+ * Returns scoring matrix from a fixed match/mismatch scoring scheme.
+ *
+ * @param match
+ * match score
+ * @param mismatch
+ * mistmatch score
+ *
+ * @return scoring matrix
+ */
+ public static Matrix generate(float match, float mismatch) {
+ float[][] scores = new float[Matrix.SIZE][Matrix.SIZE];
+
+ // Fill the matrix with the scores
+ for (int i = 0; i < Matrix.SIZE; i++) {
+ for (int j = 0; j < Matrix.SIZE; j++) {
+ if (i == j || i == 'N' || j == 'N') {
+ scores[i][j] = match;
+ } else {
+ scores[i][j] = mismatch;
+ }
+ }
+ }
+
+ // Generate some id for the matrix (hopefully to be somehow unique)
+ String id = new Long(System.currentTimeMillis()).toString();
+
+ Matrix matrix = new Matrix(id, scores);
+
+ return matrix;
+ }
+}
diff --git a/src/jaligner/matrix/MatrixLoader.java b/src/jaligner/matrix/MatrixLoader.java
index 94c4eff..650d9b5 100644
--- a/src/jaligner/matrix/MatrixLoader.java
+++ b/src/jaligner/matrix/MatrixLoader.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -28,10 +26,12 @@ import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.JarURLConnection;
import java.net.URL;
+import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Enumeration;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.jar.JarEntry;
import java.util.jar.JarFile;
@@ -41,7 +41,7 @@ import java.util.logging.Logger;
/**
* Scoring matrices loader from a jar file or a file system.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class MatrixLoader {
@@ -49,47 +49,47 @@ 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());
+ private static final Logger logger = Logger.getLogger(MatrixLoader.class
+ .getName());
/**
* Loads scoring matrix from Jar file or file system.
- * @param matrix to load
+ *
+ * @param matrix
+ * to load
* @return loaded matrix
* @throws MatrixLoaderException
* @see Matrix
*/
- public static Matrix load (String matrix) throws MatrixLoaderException {
+ public static Matrix load(String matrix) throws MatrixLoaderException {
InputStream is = null;
-
- if (new StringTokenizer(matrix, Commons.getFileSeparator()).countTokens() == 1) {
+
+ 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);
+ 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);
- }
+ 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));
@@ -97,39 +97,46 @@ public class MatrixLoader {
/**
* Loads scoring matrix from {@link InputStream}
- * @param nis named input stream
+ *
+ * @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];
-
+ public static Matrix load(NamedInputStream nis)
+ throws MatrixLoaderException {
+ logger.info("Loading scoring matrix...");
+ char[] acids = new char[Matrix.SIZE];
+
// Initialize the acids array to null values (ascii = 0)
- for (int i = 0; i < SIZE; i++) {
+ for (int i = 0; i < Matrix.SIZE; i++) {
acids[i] = 0;
}
-
- float[][] scores = new float[SIZE][SIZE];
- BufferedReader reader = new BufferedReader(new InputStreamReader(nis.getInputStream()));
-
+ float[][] scores = new float[Matrix.SIZE][Matrix.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);
- }
-
+ 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( ) );
+ tokenizer = new StringTokenizer(line.trim());
for (int j = 0; tokenizer.hasMoreTokens(); j++) {
acids[j] = tokenizer.nextToken().charAt(0);
}
@@ -137,51 +144,57 @@ public class MatrixLoader {
try {
// Read the scores
while ((line = reader.readLine()) != null) {
- tokenizer = new StringTokenizer ( line.trim( ) );
+ tokenizer = new StringTokenizer(line.trim());
char acid = tokenizer.nextToken().charAt(0);
- for (int i = 0; i < SIZE; i++) {
+ for (int i = 0; i < Matrix.SIZE; i++) {
if (acids[i] != 0) {
- scores[acid][acids[i]] = Float.parseFloat(tokenizer.nextToken());
+ 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");
+ } 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
+ *
+ * @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 {
+ public static Collection<String> list(boolean sort) throws MatrixLoaderException {
logger.info("Loading list of scoring matrices...");
- ArrayList matrices = new ArrayList();
- URL url = MatrixLoader.class.getClassLoader().getResource(MATRICES_HOME);
+ List<String> matrices = new ArrayList<String>();
+ 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();
+ 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<JarEntry> entries = jar.entries();
JarEntry entry;
String entryName;
int length = MATRICES_HOME.length();
while (entries.hasMoreElements()) {
- entry = (JarEntry) entries.nextElement();
+ entry = entries.nextElement();
if (!entry.isDirectory()) {
entryName = entry.getName();
if (entryName.startsWith(MATRICES_HOME)) {
@@ -191,19 +204,27 @@ public class MatrixLoader {
}
} else {
// Load from file system
- String home = url.getFile( );
- File dir = new File (home);
- String files[] = dir.list( );
+ String home = null;
+ try {
+ home = URLDecoder.decode(url.getFile(), "UTF-8");
+ } catch (Exception e) {
+ String message = "Failed decoding matrices url: "
+ + e.getMessage();
+ logger.log(Level.SEVERE, message, e);
+ throw new MatrixLoaderException(message);
+ }
+ 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]);
+ file = new File(home + files[i]);
if (file.isFile() && file.canRead()) {
matrices.add(file.getName());
}
}
}
if (sort) {
- Collections.sort(matrices, new MatricesCompartor());
+ Collections.sort(matrices, new MatricesCompartor());
}
logger.info("Finished loading list of scoring matrices");
return matrices;
@@ -211,10 +232,11 @@ public class MatrixLoader {
/**
* 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);
+ public static Collection<String> 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
index a62783b..0da0bae 100644
--- a/src/jaligner/matrix/MatrixLoaderException.java
+++ b/src/jaligner/matrix/MatrixLoaderException.java
@@ -1,6 +1,4 @@
/*
- * @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
@@ -20,7 +18,7 @@ package jaligner.matrix;
/**
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class MatrixLoaderException extends Exception {
diff --git a/src/jaligner/matrix/matrices/BLOSUM100 b/src/jaligner/matrix/matrices/BLOSUM100
index 4063c3b..46e9e85 100644
--- a/src/jaligner/matrix/matrices/BLOSUM100
+++ b/src/jaligner/matrix/matrices/BLOSUM100
@@ -1,31 +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
+# 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
index abf2edb..81ebd98 100644
--- a/src/jaligner/matrix/matrices/BLOSUM30
+++ b/src/jaligner/matrix/matrices/BLOSUM30
@@ -1,31 +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
+# 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
index a00a9b5..a6d99f5 100644
--- a/src/jaligner/matrix/matrices/BLOSUM35
+++ b/src/jaligner/matrix/matrices/BLOSUM35
@@ -1,31 +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
+# 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
index 41e1c63..1a4baa2 100644
--- a/src/jaligner/matrix/matrices/BLOSUM40
+++ b/src/jaligner/matrix/matrices/BLOSUM40
@@ -1,31 +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
+# 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
index ece78b5..18c3323 100644
--- a/src/jaligner/matrix/matrices/BLOSUM45
+++ b/src/jaligner/matrix/matrices/BLOSUM45
@@ -1,31 +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
+# 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
index 62592f3..3f62e3c 100644
--- a/src/jaligner/matrix/matrices/BLOSUM50
+++ b/src/jaligner/matrix/matrices/BLOSUM50
@@ -1,31 +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
+# 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
index 4a06659..c0cf3ff 100644
--- a/src/jaligner/matrix/matrices/BLOSUM55
+++ b/src/jaligner/matrix/matrices/BLOSUM55
@@ -1,31 +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
+# 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
index 45e86ca..4fd1943 100644
--- a/src/jaligner/matrix/matrices/BLOSUM60
+++ b/src/jaligner/matrix/matrices/BLOSUM60
@@ -1,31 +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
+# 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
index acb602d..205f139 100644
--- a/src/jaligner/matrix/matrices/BLOSUM62
+++ b/src/jaligner/matrix/matrices/BLOSUM62
@@ -1,31 +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
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-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
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-* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
+# 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 *
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+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
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+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
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+* -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
index 9211c16..1eacd14 100644
--- a/src/jaligner/matrix/matrices/BLOSUM65
+++ b/src/jaligner/matrix/matrices/BLOSUM65
@@ -1,31 +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
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-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
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-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
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-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
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-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
+# 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
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+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
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+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
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+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
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+* -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
index 4a05223..3e4093f 100644
--- a/src/jaligner/matrix/matrices/BLOSUM70
+++ b/src/jaligner/matrix/matrices/BLOSUM70
@@ -1,31 +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
+# 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
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+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
index 1dcf308..98964be 100644
--- a/src/jaligner/matrix/matrices/BLOSUM75
+++ b/src/jaligner/matrix/matrices/BLOSUM75
@@ -1,31 +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
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-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
+# 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 *
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+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
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+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
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+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
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+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
index d7c998b..78172a3 100644
--- a/src/jaligner/matrix/matrices/BLOSUM80
+++ b/src/jaligner/matrix/matrices/BLOSUM80
@@ -1,31 +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
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-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
+# 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
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+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
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+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
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+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
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+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
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+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
index 132ff2c..cb47fd2 100644
--- a/src/jaligner/matrix/matrices/BLOSUM85
+++ b/src/jaligner/matrix/matrices/BLOSUM85
@@ -1,31 +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
+# 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
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+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
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+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
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+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
index d5fc9e0..71441b5 100644
--- a/src/jaligner/matrix/matrices/BLOSUM90
+++ b/src/jaligner/matrix/matrices/BLOSUM90
@@ -1,31 +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
+# 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
index 0dba279..df064c8 100644
--- a/src/jaligner/matrix/matrices/BLOSUMN
+++ b/src/jaligner/matrix/matrices/BLOSUMN
@@ -1,31 +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
+# 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
index cf117a1..e287ed0 100644
--- a/src/jaligner/matrix/matrices/DAYHOFF
+++ b/src/jaligner/matrix/matrices/DAYHOFF
@@ -1,32 +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
+#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
index d35c3a8..bfec6d9 100644
--- a/src/jaligner/matrix/matrices/EDNAFULL
+++ b/src/jaligner/matrix/matrices/EDNAFULL
@@ -1,25 +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
+#
+# 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
index 038de69..d7bd4f4 100644
--- a/src/jaligner/matrix/matrices/GONNET
+++ b/src/jaligner/matrix/matrices/GONNET
@@ -1,26 +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
+# 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
index 1f22fab..63913d5 100644
--- a/src/jaligner/matrix/matrices/IDENTITY
+++ b/src/jaligner/matrix/matrices/IDENTITY
@@ -1,25 +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
+ 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
index 1895ac1..cda9e49 100644
--- a/src/jaligner/matrix/matrices/MATCH
+++ b/src/jaligner/matrix/matrices/MATCH
@@ -1,25 +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
+ 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
index 202056a..c164b06 100644
--- a/src/jaligner/matrix/matrices/PAM10
+++ b/src/jaligner/matrix/matrices/PAM10
@@ -1,34 +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
+#
+# 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
index f45c20d..2e33dd3 100644
--- a/src/jaligner/matrix/matrices/PAM100
+++ b/src/jaligner/matrix/matrices/PAM100
@@ -1,34 +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
+#
+# 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
index b2b5a44..25b2c01 100644
--- a/src/jaligner/matrix/matrices/PAM110
+++ b/src/jaligner/matrix/matrices/PAM110
@@ -1,34 +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
+#
+# 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
index 9f6a1e3..3cbb04b 100644
--- a/src/jaligner/matrix/matrices/PAM120
+++ b/src/jaligner/matrix/matrices/PAM120
@@ -1,34 +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
+#
+# 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
index d2900de..0b47a5d 100644
--- a/src/jaligner/matrix/matrices/PAM130
+++ b/src/jaligner/matrix/matrices/PAM130
@@ -1,34 +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
+#
+# 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
index 5dd4dca..022c61b 100644
--- a/src/jaligner/matrix/matrices/PAM140
+++ b/src/jaligner/matrix/matrices/PAM140
@@ -1,34 +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
+#
+# 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
index 9b64476..c010eef 100644
--- a/src/jaligner/matrix/matrices/PAM150
+++ b/src/jaligner/matrix/matrices/PAM150
@@ -1,34 +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
+#
+# 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
index e9fcd7a..f30d717 100644
--- a/src/jaligner/matrix/matrices/PAM160
+++ b/src/jaligner/matrix/matrices/PAM160
@@ -1,34 +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
+#
+# 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
index 5179b85..ca090d6 100644
--- a/src/jaligner/matrix/matrices/PAM170
+++ b/src/jaligner/matrix/matrices/PAM170
@@ -1,34 +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
+#
+# 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
index 2d8e07e..84addeb 100644
--- a/src/jaligner/matrix/matrices/PAM180
+++ b/src/jaligner/matrix/matrices/PAM180
@@ -1,34 +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
+#
+# 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
index 9dd4f3a..6840cc4 100644
--- a/src/jaligner/matrix/matrices/PAM190
+++ b/src/jaligner/matrix/matrices/PAM190
@@ -1,34 +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
+#
+# 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
index 5ced965..58cc98c 100644
--- a/src/jaligner/matrix/matrices/PAM20
+++ b/src/jaligner/matrix/matrices/PAM20
@@ -1,34 +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
+#
+# 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
index cb46b37..d4edff2 100644
--- a/src/jaligner/matrix/matrices/PAM200
+++ b/src/jaligner/matrix/matrices/PAM200
@@ -1,34 +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
+#
+# 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
index 0d485c9..0b49af5 100644
--- a/src/jaligner/matrix/matrices/PAM210
+++ b/src/jaligner/matrix/matrices/PAM210
@@ -1,34 +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
+#
+# 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
index fcaaecf..0834a92 100644
--- a/src/jaligner/matrix/matrices/PAM220
+++ b/src/jaligner/matrix/matrices/PAM220
@@ -1,34 +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
+#
+# 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
index 4ecddbe..c9ff6db 100644
--- a/src/jaligner/matrix/matrices/PAM230
+++ b/src/jaligner/matrix/matrices/PAM230
@@ -1,34 +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
+#
+# 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
index ce19219..c17cdf8 100644
--- a/src/jaligner/matrix/matrices/PAM240
+++ b/src/jaligner/matrix/matrices/PAM240
@@ -1,34 +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
+#
+# 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
index bdbb2a7..17e9e60 100644
--- a/src/jaligner/matrix/matrices/PAM250
+++ b/src/jaligner/matrix/matrices/PAM250
@@ -1,34 +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
+#
+# 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
index df46c1b..5098eb4 100644
--- a/src/jaligner/matrix/matrices/PAM260
+++ b/src/jaligner/matrix/matrices/PAM260
@@ -1,34 +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
+#
+# 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
index afd53be..322fcdb 100644
--- a/src/jaligner/matrix/matrices/PAM270
+++ b/src/jaligner/matrix/matrices/PAM270
@@ -1,34 +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
+#
+# 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
index 1662747..2b09bca 100644
--- a/src/jaligner/matrix/matrices/PAM280
+++ b/src/jaligner/matrix/matrices/PAM280
@@ -1,34 +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
+#
+# 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
index 7c139e8..6852c6a 100644
--- a/src/jaligner/matrix/matrices/PAM290
+++ b/src/jaligner/matrix/matrices/PAM290
@@ -1,34 +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
+#
+# 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
index 32202e1..8a01c88 100644
--- a/src/jaligner/matrix/matrices/PAM30
+++ b/src/jaligner/matrix/matrices/PAM30
@@ -1,34 +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
+#
+# 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
index df49f47..5d1a5a8 100644
--- a/src/jaligner/matrix/matrices/PAM300
+++ b/src/jaligner/matrix/matrices/PAM300
@@ -1,34 +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
+#
+# 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
index 03025eb..cd0e5b0 100644
--- a/src/jaligner/matrix/matrices/PAM310
+++ b/src/jaligner/matrix/matrices/PAM310
@@ -1,34 +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
+#
+# 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
index 5c4a568..d7fbbd2 100644
--- a/src/jaligner/matrix/matrices/PAM320
+++ b/src/jaligner/matrix/matrices/PAM320
@@ -1,34 +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
+#
+# 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
index 51f0d1e..77db35e 100644
--- a/src/jaligner/matrix/matrices/PAM330
+++ b/src/jaligner/matrix/matrices/PAM330
@@ -1,34 +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
+#
+# 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
index cdbec3f..02c8540 100644
--- a/src/jaligner/matrix/matrices/PAM340
+++ b/src/jaligner/matrix/matrices/PAM340
@@ -1,34 +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
+#
+# 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
index 3490108..140a6f2 100644
--- a/src/jaligner/matrix/matrices/PAM350
+++ b/src/jaligner/matrix/matrices/PAM350
@@ -1,34 +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
+#
+# 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
index f316fe0..5f6cd46 100644
--- a/src/jaligner/matrix/matrices/PAM360
+++ b/src/jaligner/matrix/matrices/PAM360
@@ -1,34 +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
+#
+# 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
index 8128be6..f72261f 100644
--- a/src/jaligner/matrix/matrices/PAM370
+++ b/src/jaligner/matrix/matrices/PAM370
@@ -1,34 +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
+#
+# 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
index a4d7e83..cbcf063 100644
--- a/src/jaligner/matrix/matrices/PAM380
+++ b/src/jaligner/matrix/matrices/PAM380
@@ -1,34 +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
+#
+# 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
index 8e9d14c..8206530 100644
--- a/src/jaligner/matrix/matrices/PAM390
+++ b/src/jaligner/matrix/matrices/PAM390
@@ -1,34 +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
+#
+# 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
index 86ff854..e0df4f6 100644
--- a/src/jaligner/matrix/matrices/PAM40
+++ b/src/jaligner/matrix/matrices/PAM40
@@ -1,34 +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
+#
+# 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
index 4945a6c..4d99c84 100644
--- a/src/jaligner/matrix/matrices/PAM400
+++ b/src/jaligner/matrix/matrices/PAM400
@@ -1,34 +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
+#
+# 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
index c2e10fa..b7c9bfd 100644
--- a/src/jaligner/matrix/matrices/PAM410
+++ b/src/jaligner/matrix/matrices/PAM410
@@ -1,34 +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
+#
+# 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
index daffa1a..53e0caf 100644
--- a/src/jaligner/matrix/matrices/PAM420
+++ b/src/jaligner/matrix/matrices/PAM420
@@ -1,34 +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
+#
+# 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
index a7e4ace..2450215 100644
--- a/src/jaligner/matrix/matrices/PAM430
+++ b/src/jaligner/matrix/matrices/PAM430
@@ -1,34 +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
+#
+# 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
index 31645b6..0429e87 100644
--- a/src/jaligner/matrix/matrices/PAM440
+++ b/src/jaligner/matrix/matrices/PAM440
@@ -1,34 +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
+#
+# 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
index 890c0ed..30cc7a2 100644
--- a/src/jaligner/matrix/matrices/PAM450
+++ b/src/jaligner/matrix/matrices/PAM450
@@ -1,34 +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
+#
+# 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
index f1d4e6b..7491d6c 100644
--- a/src/jaligner/matrix/matrices/PAM460
+++ b/src/jaligner/matrix/matrices/PAM460
@@ -1,34 +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
+#
+# 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
index df44357..9d5e333 100644
--- a/src/jaligner/matrix/matrices/PAM470
+++ b/src/jaligner/matrix/matrices/PAM470
@@ -1,34 +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
+#
+# 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
index 8c17f62..c777c62 100644
--- a/src/jaligner/matrix/matrices/PAM480
+++ b/src/jaligner/matrix/matrices/PAM480
@@ -1,34 +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
+#
+# 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
index b194d1f..107a0c8 100644
--- a/src/jaligner/matrix/matrices/PAM490
+++ b/src/jaligner/matrix/matrices/PAM490
@@ -1,34 +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
+#
+# 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
index 75aa4fb..6d37d4b 100644
--- a/src/jaligner/matrix/matrices/PAM50
+++ b/src/jaligner/matrix/matrices/PAM50
@@ -1,34 +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
+#
+# 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
index c477af8..617c3f1 100644
--- a/src/jaligner/matrix/matrices/PAM500
+++ b/src/jaligner/matrix/matrices/PAM500
@@ -1,34 +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
+#
+# 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
index 269b2f5..fba70b9 100644
--- a/src/jaligner/matrix/matrices/PAM60
+++ b/src/jaligner/matrix/matrices/PAM60
@@ -1,34 +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
+#
+# 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
index f445237..b20cdf0 100644
--- a/src/jaligner/matrix/matrices/PAM70
+++ b/src/jaligner/matrix/matrices/PAM70
@@ -1,34 +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
+#
+# 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
index d694051..55aa043 100644
--- a/src/jaligner/matrix/matrices/PAM80
+++ b/src/jaligner/matrix/matrices/PAM80
@@ -1,34 +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
+#
+# 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
index b0cc807..fa2d5b3 100644
--- a/src/jaligner/matrix/matrices/PAM90
+++ b/src/jaligner/matrix/matrices/PAM90
@@ -1,34 +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
+#
+# 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
index d5583c2..33bb485 100644
--- a/src/jaligner/matrix/package.html
+++ b/src/jaligner/matrix/package.html
@@ -1,8 +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 $--></head>
+<head></head>
<body bgcolor="white">
Scoring matrices package.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/package.html b/src/jaligner/package.html
index 614c03d..98d31fc 100644
--- a/src/jaligner/package.html
+++ b/src/jaligner/package.html
@@ -1,8 +1,8 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<html>
-<head><!--$Id: package.html,v 1.5 2004/11/25 19:07:02 ahmed Exp $--></head>
+<head></head>
<body bgcolor="white">
Core classes for the implementation of Smith-Waterman-Gotoh algorithm
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/test/AlignmentScoreChecker.java b/src/jaligner/test/AlignmentScoreChecker.java
deleted file mode 100644
index 4a57cc5..0000000
--- a/src/jaligner/test/AlignmentScoreChecker.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * $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/NeedlemanWunschGotohTester.java b/src/jaligner/test/NeedlemanWunschGotohTester.java
new file mode 100644
index 0000000..c689990
--- /dev/null
+++ b/src/jaligner/test/NeedlemanWunschGotohTester.java
@@ -0,0 +1,130 @@
+/*
+ * 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.NeedlemanWunschGotoh;
+import jaligner.Sequence;
+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.List;
+import java.util.Random;
+
+/**
+ * Testing the scores of the alignments of {@link jaligner.NeedlemanWunschGotoh}.
+ *
+ * @author Bram Minnaert
+ */
+
+public class NeedlemanWunschGotohTester {
+
+ 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 {
+ List<String> matrices = new ArrayList<String>();
+ for (Iterator<String> 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 = NeedlemanWunschGotoh.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 = NeedlemanWunschGotoh.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/NeedlemanWunschTester.java b/src/jaligner/test/NeedlemanWunschTester.java
new file mode 100644
index 0000000..2a1073e
--- /dev/null
+++ b/src/jaligner/test/NeedlemanWunschTester.java
@@ -0,0 +1,128 @@
+/*
+ * 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.NeedlemanWunsch;
+import jaligner.Sequence;
+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.List;
+import java.util.Random;
+
+/**
+ * Testing the scores of the alignments of {@link jaligner.NeedlemanWunsch}.
+ *
+ * @author Ahmed Moustafa
+ */
+
+public class NeedlemanWunschTester {
+
+ 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 {
+ List<String> matrices = new ArrayList<String>();
+ for (Iterator<String> 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);
+
+ float gap = random.nextInt(1000);
+
+ if (s1.length() > 0 && s2.length() > 0) {
+
+ Matrix matrix = (Matrix) MatrixLoader
+ .load((String) matrices.get(random
+ .nextInt(countOfMatrices)));
+ Sequence seq1 = new Sequence(s1);
+ Sequence seq2 = new Sequence(s2);
+
+ Alignment alignment1 = NeedlemanWunsch.align(seq1, seq2,
+ matrix, gap);
+
+ if (!alignment1.checkScore()) {
+ System.out.println("Invalid alignment found:");
+ System.out.println("Sequence 1 = " + s1);
+ System.out.println("Sequence 2 = " + s2);
+ System.out.println(format.format(alignment1));
+ System.out.println(alignment1.getSummary());
+ System.out
+ .println("The score of the alignment above is: "
+ + alignment1.calculateScore());
+ System.exit(1);
+ }
+
+ Alignment alignment2 = NeedlemanWunsch.align(seq2, seq1,
+ matrix, gap);
+ if (!alignment1.checkScore()) {
+ System.out.println("Invalid alignment found:");
+ System.out.println("Sequence 1 = " + s2);
+ System.out.println("Sequence 2 = " + s1);
+ System.out.println(format.format(alignment2));
+ System.out.println(alignment2.getSummary());
+ System.out
+ .println("The score of the alignment above is: "
+ + alignment2.calculateScore());
+ System.exit(1);
+ }
+
+ if (alignment1.getScore() != alignment2.getScore()) {
+ System.out.println("Not symmetric alignment:");
+
+ System.out.println("Alignment #1: ");
+ System.out.println("Sequence 1 = " + s1);
+ System.out.println("Sequence 2 = " + s2);
+ System.out.println(format.format(alignment1));
+ System.out.println(alignment1.getSummary());
+
+ System.out.println();
+
+ System.out.println("Alignment #2: ");
+ System.out.println("Sequence 1 = " + s2);
+ System.out.println("Sequence 2 = " + s1);
+ System.out.println(format.format(alignment2));
+ System.out.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
index f77c0dd..11473f3 100644
--- a/src/jaligner/test/RandomSequenceGenerator.java
+++ b/src/jaligner/test/RandomSequenceGenerator.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -27,35 +25,35 @@ import java.util.Random;
*/
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'};
-
+ 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' };
+
/**
* 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
+ *
+ * @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++) {
+ int randomInt;
+ for (int i = 0; i < length; i++) {
randomInt = random.nextInt(NUMBER_OF_CHARS);
randomChar = CHARS[randomInt];
buffer.append(randomChar);
@@ -65,11 +63,13 @@ public class RandomSequenceGenerator {
/**
* Displays 10 random protein sequences with length 50.
- * @param args no args
+ *
+ * @param args
+ * no args
*/
public static void main(String[] args) {
for (int i = 0; i < 10; i++) {
- System.out.println("S" + i + " = " + generate(50));
+ System.out.println("S" + i + " = " + generate(50));
}
}
}
\ No newline at end of file
diff --git a/src/jaligner/test/SmithWatermanGotohTester.java b/src/jaligner/test/SmithWatermanGotohTester.java
new file mode 100644
index 0000000..10f18bc
--- /dev/null
+++ b/src/jaligner/test/SmithWatermanGotohTester.java
@@ -0,0 +1,130 @@
+/*
+ * 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.List;
+import java.util.Random;
+
+/**
+ * Testing the scores of the alignments of {@link jaligner.SmithWatermanGotoh}.
+ *
+ * @author Bram Minnaert
+ */
+
+public class SmithWatermanGotohTester {
+
+ 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 {
+ List<String> matrices = new ArrayList<String>();
+ for (Iterator<String> 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/package.html b/src/jaligner/test/package.html
index 56c88e4..c290f59 100644
--- a/src/jaligner/test/package.html
+++ b/src/jaligner/test/package.html
@@ -1,6 +1,6 @@
<!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>
+<head></head>
<body bgcolor="white">
Testing package.
@author Bram Minnaert
diff --git a/src/jaligner/ui/AlignCommandLine.java b/src/jaligner/ui/AlignCommandLine.java
index bdc0df8..e70d144 100644
--- a/src/jaligner/ui/AlignCommandLine.java
+++ b/src/jaligner/ui/AlignCommandLine.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -34,7 +32,7 @@ import java.util.logging.Logger;
/**
* Command line interface for JAligner.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class AlignCommandLine {
@@ -53,7 +51,7 @@ public class AlignCommandLine {
try {
String f1 = args[0]; // file name of sequence #1
- String f2 = args[1]; // file name of sequence #1
+ String f2 = args[1]; // file name of sequence #2
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
diff --git a/src/jaligner/ui/AlignWindow.form b/src/jaligner/ui/AlignWindow.form
index 20c67ee..a36f1b6 100644
--- a/src/jaligner/ui/AlignWindow.form
+++ b/src/jaligner/ui/AlignWindow.form
@@ -1,8 +1,12 @@
<?xml version="1.0" encoding="UTF-8" ?>
-<Form version="1.0" type="org.netbeans.modules.form.forminfo.JFrameFormInfo">
+<Form version="1.2" maxVersion="1.2" type="org.netbeans.modules.form.forminfo.JFrameFormInfo">
<NonVisualComponents>
- <Menu class="javax.swing.JPopupMenu" name="jPopup">
+ <Container class="javax.swing.JPopupMenu" name="jPopup">
+
+ <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
+ <Property name="useNullLayout" type="boolean" value="true"/>
+ </Layout>
<SubComponents>
<MenuItem class="javax.swing.JMenuItem" name="jPopupOpen">
<Properties>
@@ -34,8 +38,8 @@
<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>
+ <Component class="javax.swing.JSeparator" name="jPopupSeparator1">
+ </Component>
<MenuItem class="javax.swing.JMenuItem" name="jPopupCut">
<Properties>
<Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
@@ -96,8 +100,8 @@
<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>
+ <Component class="javax.swing.JSeparator" name="jPopupSeparator2">
+ </Component>
<MenuItem class="javax.swing.JMenuItem" name="jPopupPrint">
<Properties>
<Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
@@ -113,8 +117,8 @@
<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>
+ <Component class="javax.swing.JSeparator" name="jPopupSeparator3">
+ </Component>
<MenuItem class="javax.swing.JMenuItem" name="jPopupSelectAll">
<Properties>
<Property name="accelerator" type="javax.swing.KeyStroke" editor="org.netbeans.modules.form.editors.KeyStrokeEditor">
@@ -128,7 +132,7 @@
</Events>
</MenuItem>
</SubComponents>
- </Menu>
+ </Container>
<Component class="javax.swing.ButtonGroup" name="buttonGroupSequences">
</Component>
<Menu class="javax.swing.JMenuBar" name="jMenuBar">
@@ -363,16 +367,25 @@
<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"/>
+ <Property name="name" type="java.lang.String" value="AlignWindow" noResource="true"/>
</Properties>
<SyntheticProperties>
<SyntheticProperty name="menuBar" type="java.lang.String" value="jMenuBar"/>
<SyntheticProperty name="formSizePolicy" type="int" value="1"/>
+ <SyntheticProperty name="generateCenter" type="boolean" value="false"/>
</SyntheticProperties>
<Events>
<EventHandler event="windowClosing" listener="java.awt.event.WindowListener" parameters="java.awt.event.WindowEvent" handler="exitForm"/>
</Events>
<AuxValues>
+ <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+ <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+ <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+ <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+ <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
<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>
@@ -573,13 +586,13 @@
<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"/>
+ <Font name="Courier" 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"/>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextAreaSequence1FocusGained"/>
</Events>
</Component>
</SubComponents>
@@ -626,13 +639,13 @@
<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"/>
+ <Font name="Courier" 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"/>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextAreaSequence2FocusGained"/>
</Events>
</Component>
</SubComponents>
@@ -696,14 +709,14 @@
<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"/>
+ <Font name="Courier" 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"/>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextAreaAlignmentFocusGained"/>
</Events>
</Component>
</SubComponents>
@@ -752,11 +765,14 @@
<Component class="javax.swing.JTextPane" name="jTextPaneConsole">
<Properties>
<Property name="editable" type="boolean" value="false"/>
+ <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+ <Font name="Courier" size="12" style="0"/>
+ </Property>
</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"/>
+ <EventHandler event="focusGained" listener="java.awt.event.FocusListener" parameters="java.awt.event.FocusEvent" handler="jTextPaneConsoleFocusGained"/>
</Events>
</Component>
</SubComponents>
@@ -870,7 +886,6 @@
<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>
diff --git a/src/jaligner/ui/AlignWindow.java b/src/jaligner/ui/AlignWindow.java
index 8cd7f6e..241b6db 100644
--- a/src/jaligner/ui/AlignWindow.java
+++ b/src/jaligner/ui/AlignWindow.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -21,7 +19,7 @@ package jaligner.ui;
import jaligner.Alignment;
import jaligner.Sequence;
import jaligner.SmithWatermanGotoh;
-import jaligner.example.Example;
+import jaligner.example.SmithWatermanGotohExample;
import jaligner.formats.CLUSTAL;
import jaligner.formats.FASTA;
import jaligner.formats.FormatFactory;
@@ -70,7 +68,7 @@ import javax.swing.text.JTextComponent;
/**
* Graphical user inteface for JAligner.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class AlignWindow extends javax.swing.JFrame implements ClipboardListener, DocumentListener {
@@ -117,7 +115,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
/**
* Loaded scoring matrices
*/
- private HashMap matrices = new HashMap();
+ private HashMap<String, Matrix> matrices = new HashMap<String, Matrix>();
/**
* Current text component
@@ -173,7 +171,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jFormattedTextFieldGapOpen.setValue(new Float(DEFAULT_OPEN_GAP_PENALTY));
jFormattedTextFieldGapExtend.setValue(new Float(DEFAULT_EXTEND_GAP_PENALTY));
- Collection matrices = null;
+ Collection<String> matrices = null;
try {
matrices = MatrixLoader.list(false);
} catch (Exception e) {
@@ -187,11 +185,11 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
FormatFactory.getInstance().registerFormat(new Pair());
FormatFactory.getInstance().registerFormat(new FASTA());
- Collection formats = FormatFactory.getInstance().getFormats();
+ Collection<String> formats = FormatFactory.getInstance().getFormats();
String[] outputFormats = new String[formats.size()];
- Iterator i = formats.iterator();
+ Iterator<String> i = formats.iterator();
for (int j = 0; i.hasNext(); j++) {
- outputFormats[j] = (String) i.next();
+ outputFormats[j] = i.next();
}
populateComboBox(jComboBoxOutputFormat, outputFormats, null);
@@ -235,7 +233,9 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
this.setSize(WINDOW_WIDTH, WINDOW_HEIGHT);
}
- private void initComponents() {//GEN-BEGIN:initComponents
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+ private void initComponents() {
+
jPopup = new javax.swing.JPopupMenu();
jPopupOpen = new javax.swing.JMenuItem();
jPopupSave = new javax.swing.JMenuItem();
@@ -321,7 +321,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jPopupOpenActionPerformed(evt);
}
});
-
jPopup.add(jPopupOpen);
jPopupSave.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S, java.awt.event.InputEvent.CTRL_MASK));
@@ -333,9 +332,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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));
@@ -347,7 +344,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jPopupCutActionPerformed(evt);
}
});
-
jPopup.add(jPopupCut);
jPopupCopy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK));
@@ -359,7 +355,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jPopupCopyActionPerformed(evt);
}
});
-
jPopup.add(jPopupCopy);
jPopupPaste.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK));
@@ -371,7 +366,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jPopupPasteActionPerformed(evt);
}
});
-
jPopup.add(jPopupPaste);
jPopupDelete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0));
@@ -383,9 +377,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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));
@@ -397,9 +389,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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));
@@ -410,12 +400,11 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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");
+ setName("AlignWindow"); // NOI18N
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
exitForm(evt);
@@ -431,7 +420,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonOpenActionPerformed(evt);
}
});
-
jToolBar.add(jButtonOpen);
jButtonSave.setIcon(ToolbarIcons.SAVE);
@@ -443,7 +431,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonSaveActionPerformed(evt);
}
});
-
jToolBar.add(jButtonSave);
jButtonCut.setIcon(ToolbarIcons.CUT);
@@ -455,7 +442,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonCutActionPerformed(evt);
}
});
-
jToolBar.add(jButtonCut);
jButtonCopy.setIcon(ToolbarIcons.COPY);
@@ -467,7 +453,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonCopyActionPerformed(evt);
}
});
-
jToolBar.add(jButtonCopy);
jButtonPaste.setIcon(ToolbarIcons.PASTE);
@@ -479,7 +464,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonPasteActionPerformed(evt);
}
});
-
jToolBar.add(jButtonPaste);
jButtonDelete.setIcon(ToolbarIcons.DELETE);
@@ -491,7 +475,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonDeleteActionPerformed(evt);
}
});
-
jToolBar.add(jButtonDelete);
jButtonPrint.setIcon(ToolbarIcons.PRINT);
@@ -503,7 +486,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonPrintActionPerformed(evt);
}
});
-
jToolBar.add(jButtonPrint);
jButtonExit.setIcon(ToolbarIcons.CLOSE);
@@ -515,25 +497,23 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N
jTextAreaSequence1.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
jTextAreaSequence1MouseClicked(evt);
@@ -544,7 +524,11 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jTextAreaSequence1CaretUpdate(evt);
}
});
-
+ jTextAreaSequence1.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextAreaSequence1FocusGained(evt);
+ }
+ });
jScrollPaneSequence1.setViewportView(jTextAreaSequence1);
jPanelSequence1.add(jScrollPaneSequence1, java.awt.BorderLayout.CENTER);
@@ -556,7 +540,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jRadioButtonSequence1ActionPerformed(evt);
}
});
-
jPanelSequence1.add(jRadioButtonSequence1, java.awt.BorderLayout.NORTH);
jSplitPaneSequences.setTopComponent(jPanelSequence1);
@@ -564,12 +547,8 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N
jTextAreaSequence2.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
jTextAreaSequence2MouseClicked(evt);
@@ -580,7 +559,11 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jTextAreaSequence2CaretUpdate(evt);
}
});
-
+ jTextAreaSequence2.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextAreaSequence2FocusGained(evt);
+ }
+ });
jScrollPaneSequence2.setViewportView(jTextAreaSequence2);
jPanelSequence2.add(jScrollPaneSequence2, java.awt.BorderLayout.CENTER);
@@ -592,7 +575,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jRadioButtonSequence2ActionPerformed(evt);
}
});
-
jPanelSequence2.add(jRadioButtonSequence2, java.awt.BorderLayout.NORTH);
jSplitPaneSequences.setBottomComponent(jPanelSequence2);
@@ -608,18 +590,13 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N
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);
@@ -630,7 +607,11 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jTextAreaAlignmentCaretUpdate(evt);
}
});
-
+ jTextAreaAlignment.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextAreaAlignmentFocusGained(evt);
+ }
+ });
jScrollPaneAlignment.setViewportView(jTextAreaAlignment);
jPanelAlignment.add(jScrollPaneAlignment, java.awt.BorderLayout.CENTER);
@@ -648,16 +629,12 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N
jTextPaneConsole.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
jTextPaneConsoleMouseClicked(evt);
@@ -668,7 +645,11 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jTextPaneConsoleCaretUpdate(evt);
}
});
-
+ jTextPaneConsole.addFocusListener(new java.awt.event.FocusAdapter() {
+ public void focusGained(java.awt.event.FocusEvent evt) {
+ jTextPaneConsoleFocusGained(evt);
+ }
+ });
jScrollPaneConsole.setViewportView(jTextPaneConsole);
jPanelConsole.add(jScrollPaneConsole, java.awt.BorderLayout.CENTER);
@@ -677,9 +658,9 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
getContentPane().add(jSplitPaneBody, java.awt.BorderLayout.CENTER);
+ jPanelControls.setAutoscrolls(true);
jPanelControls.setLayout(new java.awt.GridLayout(1, 0));
- jPanelControls.setAutoscrolls(true);
jLabelScoringMatrix.setDisplayedMnemonic('M');
jLabelScoringMatrix.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
jLabelScoringMatrix.setLabelFor(jComboBoxScoringMatrix);
@@ -722,7 +703,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jPanelOutputFormat.add(jLabelOutputFormat);
jComboBoxOutputFormat.setToolTipText("Alignment output format");
- jComboBoxOutputFormat.setOpaque(false);
jPanelOutputFormat.add(jComboBoxOutputFormat);
jPanelControls.add(jPanelOutputFormat);
@@ -734,7 +714,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jButtonGoActionPerformed(evt);
}
});
-
jPanelGo.add(jButtonGo);
jPanelControls.add(jPanelGo);
@@ -743,6 +722,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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');
@@ -752,7 +732,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemFileOpenActionPerformed(evt);
}
});
-
jMenuFile.add(jMenuItemFileOpen);
jMenuItemFileLoadSequence1.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_1, java.awt.event.InputEvent.CTRL_MASK));
@@ -764,7 +743,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemFileLoadSequence1ActionPerformed(evt);
}
});
-
jMenuFile.add(jMenuItemFileLoadSequence1);
jMenuItemFileLoadSequence2.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_2, java.awt.event.InputEvent.CTRL_MASK));
@@ -776,7 +754,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemFileLoadSequence2ActionPerformed(evt);
}
});
-
jMenuFile.add(jMenuItemFileLoadSequence2);
jMenuItemFileLoadMatrix.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_M, java.awt.event.InputEvent.CTRL_MASK));
@@ -789,9 +766,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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));
@@ -803,7 +778,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemFileExitActionPerformed(evt);
}
});
-
jMenuFile.add(jMenuItemFileExit);
jMenuItemFilePrint.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK));
@@ -814,13 +788,13 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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');
@@ -830,7 +804,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemEditCutActionPerformed(evt);
}
});
-
jMenuEdit.add(jMenuItemEditCut);
jMenuItemEditCopy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK));
@@ -842,7 +815,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemEditCopyActionPerformed(evt);
}
});
-
jMenuEdit.add(jMenuItemEditCopy);
jMenuItemEditPaste.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK));
@@ -854,7 +826,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemEditPasteActionPerformed(evt);
}
});
-
jMenuEdit.add(jMenuItemEditPaste);
jMenuItemEditDelete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0));
@@ -866,7 +837,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemEditDeleteActionPerformed(evt);
}
});
-
jMenuEdit.add(jMenuItemEditDelete);
jMenuItemEditSelectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK));
@@ -877,13 +847,13 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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");
@@ -893,13 +863,13 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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');
@@ -909,7 +879,6 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
jMenuItemAboutActionPerformed(evt);
}
});
-
jMenuHelp.add(jMenuItemAbout);
jMenuBar.add(jMenuHelp);
@@ -917,7 +886,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
setJMenuBar(jMenuBar);
pack();
- }//GEN-END:initComponents
+ }// </editor-fold>//GEN-END:initComponents
private void jPopupPrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupPrintActionPerformed
print();
@@ -926,8 +895,8 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
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());
+ jTextAreaSequence1.setText(SmithWatermanGotohExample.loadP53Human());
+ jTextAreaSequence2.setText(SmithWatermanGotohExample.loadP53Mouse());
align();
jTextAreaAlignment.requestFocus();
logger.info("Finished running the example...");
@@ -1170,9 +1139,9 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
}//GEN-LAST:event_jTextAreaSequence1MouseClicked
private void jMenuItemAboutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemAboutActionPerformed
- String message = "JAligner <http://jaligner.sf.net>"
+ String message = "JAligner"
+ Commons.getLineSeparator() + Commons.getLineSeparator()
- + "Open source Java implementation"
+ + "open-source Java implementation"
+ Commons.getLineSeparator()
+ "of the Smith-Waterman algorithm"
+ Commons.getLineSeparator()
@@ -1180,7 +1149,10 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
+ Commons.getLineSeparator() + Commons.getLineSeparator()
+ "Build: " + Commons.getCurrentRelease()
+ Commons.getLineSeparator() + Commons.getLineSeparator()
- + "By: Ahmed Moustafa <ahmed at users.sf.net>";
+ + "By: Ahmed Moustafa"
+ + Commons.getLineSeparator() + Commons.getLineSeparator()
+ + "https://github.com/ahmedmoustafa/JAligner";
+
JOptionPane.showMessageDialog(this, message, "About JAligner",
JOptionPane.INFORMATION_MESSAGE);
}//GEN-LAST:event_jMenuItemAboutActionPerformed
@@ -1300,9 +1272,9 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
* @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) {
+ private void populateComboBox(JComboBox combobox, Collection<String> items, String selected) {
String item;
- Iterator i = items.iterator();
+ Iterator<String> i = items.iterator();
int index = 0;
while (i.hasNext()) {
item = (String) i.next();
@@ -1577,7 +1549,7 @@ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener
setPrintControlsEnabled(enabled);
// Adjust background of the radio buttons
- Enumeration buttons = buttonGroupSequences.getElements();
+ Enumeration<AbstractButton> buttons = buttonGroupSequences.getElements();
AbstractButton button = null;
while (buttons.hasMoreElements()) {
button = (AbstractButton) buttons.nextElement();
diff --git a/src/jaligner/ui/clipboard/ClipboardHandler.java b/src/jaligner/ui/clipboard/ClipboardHandler.java
index e5020e7..49b31eb 100644
--- a/src/jaligner/ui/clipboard/ClipboardHandler.java
+++ b/src/jaligner/ui/clipboard/ClipboardHandler.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -22,7 +20,7 @@ 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)
+ * @author Ahmed Moustafa
*/
public interface ClipboardHandler {
diff --git a/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java b/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java
index 95859b7..9e3b7f2 100644
--- a/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java
+++ b/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -30,7 +28,7 @@ import java.util.logging.Logger;
/**
* Sets and gets the contents of the system clipboard.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class ClipboardHandlerAWT implements ClipboardHandler {
diff --git a/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java b/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java
index d8cbf4d..b799797 100644
--- a/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java
+++ b/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,7 +21,7 @@ import jaligner.util.Commons;
/**
* A factory for {@link jaligner.ui.clipboard.ClipboardHandler}.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class ClipboardHandlerFactory {
diff --git a/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java b/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
index e31ee47..235884b 100644
--- a/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
+++ b/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -30,7 +28,7 @@ import javax.jnlp.ServiceManager;
/**
* Sets and gets the contents of the system clipboard.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class ClipboardHandlerJNLP implements ClipboardHandler {
diff --git a/src/jaligner/ui/clipboard/ClipboardListener.java b/src/jaligner/ui/clipboard/ClipboardListener.java
index 915c64b..d3dd770 100644
--- a/src/jaligner/ui/clipboard/ClipboardListener.java
+++ b/src/jaligner/ui/clipboard/ClipboardListener.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -21,7 +19,7 @@ package jaligner.ui.clipboard;
/**
* Listener interface to get notified with the clipboard contents.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public interface ClipboardListener {
diff --git a/src/jaligner/ui/clipboard/ClipboardPoller.java b/src/jaligner/ui/clipboard/ClipboardPoller.java
index 0b4daf0..a6e1664 100644
--- a/src/jaligner/ui/clipboard/ClipboardPoller.java
+++ b/src/jaligner/ui/clipboard/ClipboardPoller.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -24,7 +22,7 @@ import java.util.logging.Logger;
/**
* Checks the system clipboard to notifies a listener with current contents.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class ClipboardPoller extends Thread {
diff --git a/src/jaligner/ui/clipboard/package.html b/src/jaligner/ui/clipboard/package.html
index d3f3582..8bf0012 100644
--- a/src/jaligner/ui/clipboard/package.html
+++ b/src/jaligner/ui/clipboard/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
Clipboard handling for JNLP and AWT.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/filechooser/FileChooser.java b/src/jaligner/ui/filechooser/FileChooser.java
index a7a1a5b..ae6546c 100644
--- a/src/jaligner/ui/filechooser/FileChooser.java
+++ b/src/jaligner/ui/filechooser/FileChooser.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,7 +21,7 @@ import java.io.InputStream;
/**
* Opens and saves files.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public abstract class FileChooser {
diff --git a/src/jaligner/ui/filechooser/FileChooserException.java b/src/jaligner/ui/filechooser/FileChooserException.java
index 3882735..f9ec772 100644
--- a/src/jaligner/ui/filechooser/FileChooserException.java
+++ b/src/jaligner/ui/filechooser/FileChooserException.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -21,7 +19,7 @@ package jaligner.ui.filechooser;
/**
* File chooser exception
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class FileChooserException extends Exception {
diff --git a/src/jaligner/ui/filechooser/FileChooserFactory.java b/src/jaligner/ui/filechooser/FileChooserFactory.java
index 867db72..d3897ff 100644
--- a/src/jaligner/ui/filechooser/FileChooserFactory.java
+++ b/src/jaligner/ui/filechooser/FileChooserFactory.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,7 +21,7 @@ import jaligner.util.Commons;
/**
* A factory for {@link jaligner.ui.filechooser.FileChooser}.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class FileChooserFactory {
diff --git a/src/jaligner/ui/filechooser/FileChooserJNLP.java b/src/jaligner/ui/filechooser/FileChooserJNLP.java
index d794034..88fcd21 100644
--- a/src/jaligner/ui/filechooser/FileChooserJNLP.java
+++ b/src/jaligner/ui/filechooser/FileChooserJNLP.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -29,7 +27,7 @@ import javax.jnlp.ServiceManager;
/**
* Opens and saves files.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class FileChooserJNLP extends FileChooser {
diff --git a/src/jaligner/ui/filechooser/FileChooserTrusted.java b/src/jaligner/ui/filechooser/FileChooserTrusted.java
index 5ebd6ff..1a41c69 100644
--- a/src/jaligner/ui/filechooser/FileChooserTrusted.java
+++ b/src/jaligner/ui/filechooser/FileChooserTrusted.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -31,7 +29,7 @@ import javax.swing.JFileChooser;
/**
* Opens and saves files.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class FileChooserTrusted extends FileChooser {
diff --git a/src/jaligner/ui/filechooser/NamedInputStream.java b/src/jaligner/ui/filechooser/NamedInputStream.java
index 6ee46ac..911580c 100644
--- a/src/jaligner/ui/filechooser/NamedInputStream.java
+++ b/src/jaligner/ui/filechooser/NamedInputStream.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -23,7 +21,7 @@ import java.io.Serializable;
/**
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class NamedInputStream extends Object implements Serializable {
diff --git a/src/jaligner/ui/filechooser/package.html b/src/jaligner/ui/filechooser/package.html
index 437cb06..260571a 100644
--- a/src/jaligner/ui/filechooser/package.html
+++ b/src/jaligner/ui/filechooser/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
File loading and storing.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/images/ToolbarIcons.java b/src/jaligner/ui/images/ToolbarIcons.java
index 4864d27..f6a8332 100644
--- a/src/jaligner/ui/images/ToolbarIcons.java
+++ b/src/jaligner/ui/images/ToolbarIcons.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -22,7 +20,8 @@ import javax.swing.ImageIcon;
/**
* Toolbar icons
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ *
+ * @author Ahmed Moustafa
*/
public abstract class ToolbarIcons {
diff --git a/src/jaligner/ui/images/package.html b/src/jaligner/ui/images/package.html
index 5c792c9..b9181cd 100644
--- a/src/jaligner/ui/images/package.html
+++ b/src/jaligner/ui/images/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
Images used in the toolbar.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/logging/DocumentHandler.java b/src/jaligner/ui/logging/DocumentHandler.java
index b96c775..30aaa70 100644
--- a/src/jaligner/ui/logging/DocumentHandler.java
+++ b/src/jaligner/ui/logging/DocumentHandler.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -32,7 +30,7 @@ import javax.swing.text.StyledDocument;
/**
* Logging handler of {@link javax.swing.JTextPane}.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class DocumentHandler extends Handler {
diff --git a/src/jaligner/ui/logging/RecordFormatter.java b/src/jaligner/ui/logging/RecordFormatter.java
index bae1955..b7209d2 100644
--- a/src/jaligner/ui/logging/RecordFormatter.java
+++ b/src/jaligner/ui/logging/RecordFormatter.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -26,7 +24,7 @@ import java.util.logging.LogRecord;
/**
* Logging record formatter
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class RecordFormatter extends Formatter {
diff --git a/src/jaligner/ui/logging/package.html b/src/jaligner/ui/logging/package.html
index 4506adc..268f9fe 100644
--- a/src/jaligner/ui/logging/package.html
+++ b/src/jaligner/ui/logging/package.html
@@ -1,8 +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 $--></head>
+<head></head>
<body bgcolor="white">
Logging package.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/package.html b/src/jaligner/ui/package.html
index cf56259..3d30727 100644
--- a/src/jaligner/ui/package.html
+++ b/src/jaligner/ui/package.html
@@ -1,8 +1,8 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<html>
-<head><!--$Id: package.html,v 1.5 2005/04/05 13:43:32 ahmed Exp $--></head>
+<head></head>
<body bgcolor="white">
Command line and graphical user interface.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/ui/util/PrintJobMointor.java b/src/jaligner/ui/util/PrintJobMointor.java
index 8329caa..f6ca0c4 100644
--- a/src/jaligner/ui/util/PrintJobMointor.java
+++ b/src/jaligner/ui/util/PrintJobMointor.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -28,7 +26,7 @@ import javax.print.event.PrintJobEvent;
/**
* Mointor for print job.
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class PrintJobMointor {
diff --git a/src/jaligner/ui/util/TextComponentUtil.java b/src/jaligner/ui/util/TextComponentUtil.java
index 954f64b..8df1fef 100644
--- a/src/jaligner/ui/util/TextComponentUtil.java
+++ b/src/jaligner/ui/util/TextComponentUtil.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -50,7 +48,7 @@ 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)
+ * @author Ahmed Moustafa
*/
public class TextComponentUtil {
diff --git a/src/jaligner/ui/util/TextComponentUtilException.java b/src/jaligner/ui/util/TextComponentUtilException.java
index d99df09..815db22 100644
--- a/src/jaligner/ui/util/TextComponentUtilException.java
+++ b/src/jaligner/ui/util/TextComponentUtilException.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -20,7 +18,7 @@ package jaligner.ui.util;
/**
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class TextComponentUtilException extends Exception {
diff --git a/src/jaligner/ui/util/package.html b/src/jaligner/ui/util/package.html
index a98316d..28c5294 100644
--- a/src/jaligner/ui/util/package.html
+++ b/src/jaligner/ui/util/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
Text component utilites package.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
diff --git a/src/jaligner/util/Commons.java b/src/jaligner/util/Commons.java
index 8bf93c3..f5838e8 100644
--- a/src/jaligner/util/Commons.java
+++ b/src/jaligner/util/Commons.java
@@ -1,6 +1,4 @@
/*
- * $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
@@ -27,13 +25,18 @@ import java.util.logging.Level;
import java.util.logging.Logger;
/**
- * Global constants/varilables/settings
+ * Global constants/variables/settings
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public abstract class Commons {
/**
+ * Tab
+ */
+ public static final String TAB = "\t";
+
+ /**
* Logger
*/
private static final Logger logger = Logger.getLogger(Commons.class
@@ -211,7 +214,6 @@ public abstract class Commons {
* @return information about JAligner
*/
public static String getJAlignerInfo() {
- return "JAligner - Build: " + getCurrentRelease()
- + " - By: Ahmed Moustafa (ahmed at users.sf.net)";
+ return "JAligner - Build: " + getCurrentRelease() + " - By: Ahmed Moustafa";
}
}
\ No newline at end of file
diff --git a/src/jaligner/util/SequenceParser.java b/src/jaligner/util/SequenceParser.java
index 27ee681..6a0c2b0 100644
--- a/src/jaligner/util/SequenceParser.java
+++ b/src/jaligner/util/SequenceParser.java
@@ -1,6 +1,4 @@
/*
- * @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
@@ -32,13 +30,13 @@ import java.util.logging.Logger;
/**
* SequenceParser to sequences from different formats.
* <br>
- * Currently the supported formats are:
+ * The supported formats are:
* <ul>
- * <li>Plain sequence</li>
- * <li><a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">Sequence</a></li>
+ * <li>Plain sequence</li>, and
+ * <li><a href="http://en.wikipedia.org/wiki/FASTA_format">FASTA</a></li>
* </ul>
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class SequenceParser {
diff --git a/src/jaligner/util/SequenceParserException.java b/src/jaligner/util/SequenceParserException.java
index 450169f..1957f2b 100644
--- a/src/jaligner/util/SequenceParserException.java
+++ b/src/jaligner/util/SequenceParserException.java
@@ -1,6 +1,4 @@
/*
- * @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
@@ -20,7 +18,7 @@ package jaligner.util;
/**
*
- * @author Ahmed Moustafa (ahmed at users.sf.net)
+ * @author Ahmed Moustafa
*/
public class SequenceParserException extends Exception {
diff --git a/src/jaligner/util/package.html b/src/jaligner/util/package.html
index 9223585..6316731 100644
--- a/src/jaligner/util/package.html
+++ b/src/jaligner/util/package.html
@@ -1,8 +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>
+<head></head>
<body bgcolor="white">
Utility classes for helping core and GUI classes.
- at author Ahmed Moustafa (ahmed at users.sf.net)
+ at author Ahmed Moustafa
</body>
</html>
\ No newline at end of file
--
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