[jalview] 01/08: Merge tag 'upstream/2.7.dfsg'
Emmanuel Bourg
ebourg-guest at moszumanska.debian.org
Fri Sep 12 12:56:46 UTC 2014
This is an automated email from the git hooks/post-receive script.
ebourg-guest pushed a commit to branch master
in repository jalview.
commit 80665ce8ffb74cd42e9af41a8d096a8d6690c011
Merge: 7c4c6df 1bf52fe
Author: Emmanuel Bourg <ebourg at apache.org>
Date: Fri Sep 12 14:04:14 2014 +0200
Merge tag 'upstream/2.7.dfsg'
Upstream version 2.7.dfsg
JalviewApplet.jpx | 75 +
JalviewX.jpx | 47 +
LICENSE | 621 +++
README | 39 +
build.xml | 595 +++
doc/AddingGroovySupport.html | 60 +
doc/building.html | 99 +
doc/developing.html | 41 +
doc/index.html | 153 +
doc/newdmobj.html | 36 +
help/help.hs | 43 +
help/help.jhm | 106 +
help/helpTOC.html | 97 +
help/helpTOC.xml | 131 +
help/html/align.jpg | Bin 0 -> 14648 bytes
help/html/calculations/consensus.html | 35 +
help/html/calculations/conservation.html | 44 +
help/html/calculations/pairwise.html | 37 +
help/html/calculations/pca.html | 84 +
help/html/calculations/quality.html | 49 +
help/html/calculations/recoverInputdata.html | 30 +
help/html/calculations/redundancy.html | 33 +
help/html/calculations/sorting.html | 72 +
help/html/calculations/tree.html | 85 +
help/html/calculations/treeviewer.html | 117 +
help/html/colourSchemes/abovePID.html | 37 +
.../html/colourSchemes/annotationColourSetting.jpg | Bin 0 -> 43293 bytes
help/html/colourSchemes/annotationColouring.html | 61 +
help/html/colourSchemes/annotationColours.jpg | Bin 0 -> 107885 bytes
help/html/colourSchemes/blosum.html | 37 +
help/html/colourSchemes/buried.html | 69 +
help/html/colourSchemes/clustal.html | 62 +
help/html/colourSchemes/conservation.html | 44 +
help/html/colourSchemes/helix.html | 69 +
help/html/colourSchemes/hydrophobic.html | 72 +
help/html/colourSchemes/index.html | 297 ++
help/html/colourSchemes/nucleotide.html | 42 +
help/html/colourSchemes/pid.html | 50 +
help/html/colourSchemes/strand.html | 69 +
help/html/colourSchemes/taylor.html | 68 +
help/html/colourSchemes/textcolour.gif | Bin 0 -> 21788 bytes
help/html/colourSchemes/textcolour.html | 37 +
help/html/colourSchemes/turn.html | 69 +
help/html/colourSchemes/user.html | 39 +
help/html/colourSchemes/userDefined.gif | Bin 0 -> 35269 bytes
help/html/colourSchemes/zappo.html | 67 +
help/html/editing/editing.jpg | Bin 0 -> 42427 bytes
help/html/editing/index.html | 73 +
help/html/features/amendfeature.gif | Bin 0 -> 28030 bytes
help/html/features/annotation.html | 108 +
help/html/features/annotationsFormat.html | 209 +
help/html/features/clarguments.html | 196 +
help/html/features/codingfeatures.html | 33 +
help/html/features/commandline.html | 52 +
help/html/features/creatinFeatures.html | 55 +
help/html/features/crnewfeature.gif | Bin 0 -> 24348 bytes
help/html/features/cursorMode.html | 72 +
help/html/features/das.gif | Bin 0 -> 37535 bytes
help/html/features/dasfeatures.html | 62 +
help/html/features/dassettings.html | 54 +
help/html/features/editingFeatures.html | 43 +
help/html/features/exportannot.gif | Bin 0 -> 8555 bytes
help/html/features/fcsgtthan.gif | Bin 0 -> 136 bytes
help/html/features/fcsltthan.gif | Bin 0 -> 136 bytes
help/html/features/fcsminmax.gif | Bin 0 -> 104 bytes
help/html/features/fcsntlabel.gif | Bin 0 -> 121 bytes
help/html/features/featureSettings.gif | Bin 0 -> 23195 bytes
help/html/features/featurecoloursettings.gif | Bin 0 -> 8518 bytes
help/html/features/featuresFormat.html | 215 +
help/html/features/featureschemes.html | 73 +
help/html/features/featuresettings.html | 79 +
help/html/features/groovy.html | 94 +
help/html/features/hiddenRegions.html | 98 +
help/html/features/jalarchive.html | 38 +
help/html/features/jmol.html | 214 +
help/html/features/multipleViews.html | 76 +
help/html/features/newkeystrokes.html | 50 +
help/html/features/overview.gif | Bin 0 -> 10356 bytes
help/html/features/overview.html | 29 +
help/html/features/pdbviewer.html | 160 +
help/html/features/preferences.html | 177 +
help/html/features/search.gif | Bin 0 -> 5043 bytes
help/html/features/search.html | 116 +
help/html/features/seqfeatures.html | 81 +
help/html/features/seqfetch.html | 72 +
help/html/features/seqfetcher.gif | Bin 0 -> 8702 bytes
help/html/features/seqmappings.html | 39 +
help/html/features/viewingpdbs.html | 121 +
help/html/features/wrap.html | 335 ++
help/html/index.html | 36 +
help/html/io/export.html | 57 +
help/html/io/file.png | Bin 0 -> 590 bytes
help/html/io/fileformats.html | 72 +
help/html/io/index.html | 74 +
help/html/io/modellerpir.html | 62 +
help/html/jalviewjnlp.html | 78 +
help/html/keys.html | 264 +
help/html/memory.html | 118 +
help/html/menus/alignmentMenu.html | 567 +++
help/html/menus/alwannotations.html | 87 +
help/html/menus/alwcalculate.html | 93 +
help/html/menus/alwcolour.html | 61 +
help/html/menus/alwedit.html | 101 +
help/html/menus/alwfile.html | 111 +
help/html/menus/alwformat.html | 79 +
help/html/menus/alwselect.html | 48 +
help/html/menus/alwview.html | 91 +
help/html/menus/desktopMenu.html | 126 +
help/html/menus/index.html | 39 +
help/html/menus/popupMenu.html | 166 +
help/html/menus/wsmenu.html | 90 +
help/html/misc/aaproperties.html | 48 +
help/html/misc/ala.jpg | Bin 0 -> 2039 bytes
help/html/misc/aminoAcids.html | 308 ++
help/html/misc/arg.jpg | Bin 0 -> 4445 bytes
help/html/misc/asparagine.jpg | Bin 0 -> 3212 bytes
help/html/misc/aspartate.jpg | Bin 0 -> 2824 bytes
help/html/misc/cys.jpg | Bin 0 -> 2360 bytes
help/html/misc/geneticCode.html | 92 +
help/html/misc/glutamate.jpg | Bin 0 -> 3341 bytes
help/html/misc/glutamine.jpg | Bin 0 -> 3546 bytes
help/html/misc/gly.jpg | Bin 0 -> 1823 bytes
help/html/misc/his.jpg | Bin 0 -> 3673 bytes
help/html/misc/iso.jpg | Bin 0 -> 3613 bytes
help/html/misc/leu.jpg | Bin 0 -> 3483 bytes
help/html/misc/lys.jpg | Bin 0 -> 3912 bytes
help/html/misc/met.jpg | Bin 0 -> 3365 bytes
help/html/misc/phe.jpg | Bin 0 -> 3148 bytes
help/html/misc/pro.jpg | Bin 0 -> 3037 bytes
help/html/misc/properties.gif | Bin 0 -> 29022 bytes
help/html/misc/ser.jpg | Bin 0 -> 2203 bytes
help/html/misc/thr.jpg | Bin 0 -> 2850 bytes
help/html/misc/tryp.jpg | Bin 0 -> 4450 bytes
help/html/misc/tyr.jpg | Bin 0 -> 3500 bytes
help/html/misc/val.jpg | Bin 0 -> 3024 bytes
help/html/privacy.html | 76 +
help/html/releases.html | 1139 +++++
help/html/vamsas/index.html | 136 +
help/html/webServices/JABAWS.html | 61 +
help/html/webServices/clwqueued.gif | Bin 0 -> 5619 bytes
help/html/webServices/dbreffetcher.html | 77 +
help/html/webServices/index.html | 97 +
help/html/webServices/invalidurldialog.gif | Bin 0 -> 9370 bytes
help/html/webServices/jalviewrssreader.gif | Bin 0 -> 24576 bytes
help/html/webServices/jnet.html | 116 +
help/html/webServices/jnetprediction.gif | Bin 0 -> 14715 bytes
help/html/webServices/msaclient.html | 75 +
help/html/webServices/multimafftjbs.gif | Bin 0 -> 7301 bytes
help/html/webServices/newsreader.html | 28 +
help/html/webServices/shmr.html | 65 +
help/html/webServices/urllinks.html | 89 +
help/html/webServices/webServicesParams.html | 86 +
help/html/webServices/webServicesPrefs.html | 79 +
help/html/webServices/wsparams.gif | Bin 0 -> 19287 bytes
help/html/webServices/wsprefs.gif | Bin 0 -> 18473 bytes
help/html/whatsNew.html | 103 +
help/icons/Home.png | Bin 0 -> 1598 bytes
help/icons/back.png | Bin 0 -> 1315 bytes
help/icons/forward.png | Bin 0 -> 1303 bytes
help/icons/print.png | Bin 0 -> 1405 bytes
help/icons/setup.png | Bin 0 -> 1514 bytes
jalview-jalopy.xml | 393 ++
nbbuild.xml | 98 +
nbproject/genfiles.properties | 25 +
nbproject/project.properties | 143 +
nbproject/project.xml | 30 +
resources/embl_mapping.xml | 158 +
resources/images/file.png | Bin 0 -> 590 bytes
resources/images/idwidth.gif | Bin 0 -> 166 bytes
resources/images/link.gif | Bin 0 -> 320 bytes
resources/images/logo.gif | Bin 0 -> 615 bytes
resources/images/logo_big.gif | Bin 0 -> 6804 bytes
resources/uniprot_mapping.xml | 96 +
schemas/JalviewUserColours.xsd | 50 +
schemas/JalviewWsParamSet.xsd | 74 +
schemas/castor-mapping.xsd | 314 ++
schemas/jalview.nodesc.properties | 30 +
schemas/jalview.properties | 30 +
schemas/jalview.xsd | 304 ++
schemas/jalviewJvV1.xsd | 162 +
schemas/vamsas.xsd | 268 +
schemas/vamsasJvV1.xsd | 91 +
src/MCview/AppletPDBCanvas.java | 1202 +++++
src/MCview/AppletPDBViewer.java | 255 +
src/MCview/Atom.java | 105 +
src/MCview/Bond.java | 79 +
src/MCview/MCMatrix.java | 174 +
src/MCview/PDBCanvas.java | 1167 +++++
src/MCview/PDBChain.java | 514 ++
src/MCview/PDBViewer.java | 694 +++
src/MCview/PDBfile.java | 266 +
src/MCview/Residue.java | 51 +
src/MCview/Zsort.java | 72 +
src/com/stevesoft/pat/AmpersandRule.java | 30 +
src/com/stevesoft/pat/Any.java | 55 +
src/com/stevesoft/pat/BackG.java | 47 +
src/com/stevesoft/pat/BackMatch.java | 57 +
src/com/stevesoft/pat/BackRefRule.java | 40 +
src/com/stevesoft/pat/Backup.java | 54 +
src/com/stevesoft/pat/BasicStringBufferLike.java | 23 +
src/com/stevesoft/pat/Bits.java | 3040 ++++++++++++
src/com/stevesoft/pat/Boundary.java | 89 +
src/com/stevesoft/pat/Bracket.java | 88 +
src/com/stevesoft/pat/CaseMgr.java | 4409 +++++++++++++++++
src/com/stevesoft/pat/ChangeRule.java | 50 +
src/com/stevesoft/pat/CodeRule.java | 33 +
src/com/stevesoft/pat/Ctrl.java | 61 +
src/com/stevesoft/pat/Custom.java | 64 +
src/com/stevesoft/pat/CustomEndpoint.java | 44 +
src/com/stevesoft/pat/DirFileRegex.java | 31 +
src/com/stevesoft/pat/DotMulti.java | 209 +
src/com/stevesoft/pat/End.java | 71 +
src/com/stevesoft/pat/FastBracket.java | 256 +
src/com/stevesoft/pat/FastMulti.java | 169 +
src/com/stevesoft/pat/FileRegex.java | 323 ++
src/com/stevesoft/pat/Group.java | 77 +
src/com/stevesoft/pat/LeftRule.java | 31 +
src/com/stevesoft/pat/Multi.java | 90 +
src/com/stevesoft/pat/MultiMin.java | 21 +
src/com/stevesoft/pat/Multi_stage2.java | 157 +
src/com/stevesoft/pat/NoPattern.java | 33 +
src/com/stevesoft/pat/NonDirFileRegex.java | 31 +
src/com/stevesoft/pat/NotImplementedError.java | 16 +
src/com/stevesoft/pat/NullPattern.java | 37 +
src/com/stevesoft/pat/NullRule.java | 30 +
src/com/stevesoft/pat/Or.java | 130 +
src/com/stevesoft/pat/OrMark.java | 73 +
src/com/stevesoft/pat/PartialBuffer.java | 109 +
src/com/stevesoft/pat/Pattern.java | 294 ++
src/com/stevesoft/pat/PatternSub.java | 16 +
src/com/stevesoft/pat/PopRule.java | 24 +
src/com/stevesoft/pat/Prop.java | 75 +
src/com/stevesoft/pat/Pthings.java | 47 +
src/com/stevesoft/pat/PushRule.java | 50 +
src/com/stevesoft/pat/RBuffer.java | 52 +
src/com/stevesoft/pat/Range.java | 97 +
src/com/stevesoft/pat/RegOpt.java | 448 ++
src/com/stevesoft/pat/RegRes.java | 299 ++
src/com/stevesoft/pat/RegSyntax.java | 30 +
src/com/stevesoft/pat/RegSyntaxError.java | 40 +
src/com/stevesoft/pat/Regex.java | 2085 ++++++++
src/com/stevesoft/pat/RegexReader.java | 309 ++
src/com/stevesoft/pat/RegexTokenizer.java | 171 +
src/com/stevesoft/pat/RegexWriter.java | 276 ++
src/com/stevesoft/pat/ReplaceRule.java | 400 ++
src/com/stevesoft/pat/Replacer.java | 367 ++
src/com/stevesoft/pat/RightRule.java | 31 +
src/com/stevesoft/pat/Rthings.java | 68 +
src/com/stevesoft/pat/RuleHolder.java | 43 +
src/com/stevesoft/pat/Skip.java | 196 +
src/com/stevesoft/pat/Skip2.java | 57 +
src/com/stevesoft/pat/SkipBMH.java | 279 ++
src/com/stevesoft/pat/Skipped.java | 56 +
src/com/stevesoft/pat/SpecialRule.java | 19 +
src/com/stevesoft/pat/Start.java | 56 +
src/com/stevesoft/pat/StrPos.java | 192 +
src/com/stevesoft/pat/StringBufferLike.java | 92 +
src/com/stevesoft/pat/StringLike.java | 47 +
src/com/stevesoft/pat/StringRule.java | 39 +
src/com/stevesoft/pat/SubMark.java | 32 +
src/com/stevesoft/pat/TransPat.java | 51 +
src/com/stevesoft/pat/Transformer.java | 233 +
src/com/stevesoft/pat/UniValidator.java | 24 +
src/com/stevesoft/pat/Validator.java | 75 +
src/com/stevesoft/pat/WantMoreTextReplaceRule.java | 29 +
src/com/stevesoft/pat/lookAhead.java | 99 +
src/com/stevesoft/pat/oneChar.java | 76 +
src/com/stevesoft/pat/parsePerl.java | 373 ++
src/com/stevesoft/pat/patInf.java | 16 +
src/com/stevesoft/pat/patInt.java | 180 +
.../stevesoft/pat/wrap/CharArrayBufferWrap.java | 54 +
src/com/stevesoft/pat/wrap/CharArrayWrap.java | 75 +
.../stevesoft/pat/wrap/RandomAccessFileWrap.java | 170 +
src/com/stevesoft/pat/wrap/StringBufferWrap.java | 49 +
src/com/stevesoft/pat/wrap/StringWrap.java | 59 +
src/com/stevesoft/pat/wrap/WriterWrap.java | 61 +
src/ext/vamsas/IRegistry.java | 24 +
src/ext/vamsas/IRegistryService.java | 29 +
src/ext/vamsas/IRegistryServiceLocator.java | 183 +
src/ext/vamsas/Jpred.java | 34 +
src/ext/vamsas/JpredService.java | 28 +
src/ext/vamsas/JpredServiceLocator.java | 181 +
src/ext/vamsas/JpredSoapBindingStub.java | 413 ++
src/ext/vamsas/MuscleWS.java | 34 +
src/ext/vamsas/MuscleWSService.java | 29 +
src/ext/vamsas/MuscleWSServiceLocator.java | 190 +
src/ext/vamsas/MuscleWSSoapBindingStub.java | 458 ++
src/ext/vamsas/RegistryServiceSoapBindingStub.java | 230 +
src/ext/vamsas/SeqSearchI.java | 37 +
src/ext/vamsas/SeqSearchServiceLocator.java | 183 +
src/ext/vamsas/SeqSearchServiceService.java | 29 +
.../vamsas/SeqSearchServiceSoapBindingStub.java | 488 ++
src/ext/vamsas/ServiceHandle.java | 254 +
src/ext/vamsas/ServiceHandles.java | 154 +
src/jalview/analysis/AAFrequency.java | 336 ++
src/jalview/analysis/AlignSeq.java | 921 ++++
src/jalview/analysis/AlignmentSorter.java | 949 ++++
src/jalview/analysis/Conservation.java | 698 +++
src/jalview/analysis/CrossRef.java | 598 +++
src/jalview/analysis/Dna.java | 716 +++
src/jalview/analysis/Finder.java | 358 ++
src/jalview/analysis/Grouping.java | 207 +
src/jalview/analysis/NJTree.java | 1377 ++++++
src/jalview/analysis/PCA.java | 255 +
src/jalview/analysis/ParseProperties.java | 180 +
src/jalview/analysis/SeqsetUtils.java | 300 ++
src/jalview/analysis/SequenceIdMatcher.java | 312 ++
src/jalview/api/AlignmentViewPanel.java | 34 +
src/jalview/api/FeatureRenderer.java | 37 +
src/jalview/api/SequenceRenderer.java | 29 +
src/jalview/api/SequenceStructureBinding.java | 31 +
.../api/StructureSelectionManagerProvider.java | 27 +
src/jalview/appletgui/APopupMenu.java | 1066 ++++
src/jalview/appletgui/AlignFrame.java | 3583 ++++++++++++++
src/jalview/appletgui/AlignViewport.java | 1761 +++++++
src/jalview/appletgui/AlignmentPanel.java | 983 ++++
src/jalview/appletgui/AnnotationColourChooser.java | 546 +++
src/jalview/appletgui/AnnotationLabels.java | 713 +++
src/jalview/appletgui/AnnotationPanel.java | 1287 +++++
src/jalview/appletgui/AppletJmol.java | 656 +++
src/jalview/appletgui/AppletJmolBinding.java | 181 +
src/jalview/appletgui/CutAndPasteTransfer.java | 277 ++
src/jalview/appletgui/EditNameDialog.java | 76 +
src/jalview/appletgui/EmbmenuFrame.java | 314 ++
src/jalview/appletgui/ExtJmol.java | 195 +
src/jalview/appletgui/FeatureColourChooser.java | 439 ++
src/jalview/appletgui/FeatureRenderer.java | 1266 +++++
src/jalview/appletgui/FeatureSettings.java | 834 ++++
src/jalview/appletgui/Finder.java | 260 +
src/jalview/appletgui/FontChooser.java | 281 ++
src/jalview/appletgui/IdCanvas.java | 373 ++
src/jalview/appletgui/IdPanel.java | 480 ++
src/jalview/appletgui/IdwidthAdjuster.java | 107 +
src/jalview/appletgui/JVDialog.java | 77 +
src/jalview/appletgui/OverviewPanel.java | 453 ++
src/jalview/appletgui/PCAPanel.java | 324 ++
src/jalview/appletgui/PaintRefresher.java | 249 +
src/jalview/appletgui/PairwiseAlignPanel.java | 170 +
src/jalview/appletgui/RedundancyPanel.java | 325 ++
src/jalview/appletgui/RotatableCanvas.java | 643 +++
src/jalview/appletgui/ScalePanel.java | 456 ++
src/jalview/appletgui/SeqCanvas.java | 815 ++++
src/jalview/appletgui/SeqPanel.java | 1815 +++++++
src/jalview/appletgui/SequenceRenderer.java | 362 ++
src/jalview/appletgui/SliderPanel.java | 376 ++
src/jalview/appletgui/Tooltip.java | 233 +
src/jalview/appletgui/TreeCanvas.java | 679 +++
src/jalview/appletgui/TreePanel.java | 381 ++
src/jalview/appletgui/UserDefinedColours.java | 687 +++
src/jalview/bin/Cache.java | 805 +++
src/jalview/bin/Jalview.java | 1024 ++++
src/jalview/bin/JalviewLite.java | 2686 ++++++++++
src/jalview/bin/JalviewLiteURLRetrieve.java | 144 +
src/jalview/binding/Alignment.java | 186 +
src/jalview/binding/Annotation.java | 449 ++
src/jalview/binding/AnnotationElement.java | 308 ++
src/jalview/binding/Colour.java | 500 ++
src/jalview/binding/Feature.java | 307 ++
src/jalview/binding/FeatureSettings.java | 292 ++
src/jalview/binding/Features.java | 133 +
src/jalview/binding/JGroup.java | 756 +++
src/jalview/binding/JSeq.java | 640 +++
src/jalview/binding/JalviewModel.java | 237 +
src/jalview/binding/JalviewModelSequence.java | 939 ++++
src/jalview/binding/JalviewUserColours.java | 347 ++
src/jalview/binding/Pdbentry.java | 343 ++
src/jalview/binding/PdbentryItem.java | 209 +
src/jalview/binding/Pdbids.java | 133 +
src/jalview/binding/Property.java | 186 +
src/jalview/binding/Sequence.java | 133 +
src/jalview/binding/SequenceSet.java | 531 ++
src/jalview/binding/SequenceType.java | 211 +
src/jalview/binding/Setting.java | 267 +
src/jalview/binding/Tree.java | 837 ++++
src/jalview/binding/UserColourScheme.java | 133 +
src/jalview/binding/UserColours.java | 186 +
src/jalview/binding/VAMSAS.java | 598 +++
src/jalview/binding/VamsasModel.java | 133 +
src/jalview/binding/Viewport.java | 1449 ++++++
src/jalview/commands/ChangeCaseCommand.java | 137 +
src/jalview/commands/CommandI.java | 29 +
src/jalview/commands/EditCommand.java | 923 ++++
src/jalview/commands/OrderCommand.java | 61 +
src/jalview/commands/RemoveGapColCommand.java | 116 +
src/jalview/commands/RemoveGapsCommand.java | 129 +
src/jalview/commands/SlideSequencesCommand.java | 85 +
src/jalview/commands/TrimRegionCommand.java | 171 +
src/jalview/datamodel/AlignedCodonFrame.java | 318 ++
src/jalview/datamodel/Alignment.java | 1285 +++++
src/jalview/datamodel/AlignmentAnnotation.java | 826 ++++
src/jalview/datamodel/AlignmentI.java | 425 ++
src/jalview/datamodel/AlignmentOrder.java | 326 ++
src/jalview/datamodel/AlignmentView.java | 1175 +++++
src/jalview/datamodel/Annotation.java | 120 +
src/jalview/datamodel/BinaryNode.java | 299 ++
src/jalview/datamodel/BinarySequence.java | 168 +
src/jalview/datamodel/CigarArray.java | 379 ++
src/jalview/datamodel/CigarBase.java | 646 +++
src/jalview/datamodel/CigarCigar.java | 61 +
src/jalview/datamodel/CigarSimple.java | 32 +
src/jalview/datamodel/ColumnSelection.java | 1245 +++++
src/jalview/datamodel/DBRefEntry.java | 183 +
src/jalview/datamodel/DBRefSource.java | 133 +
src/jalview/datamodel/FeatureProperties.java | 48 +
src/jalview/datamodel/GraphLine.java | 54 +
src/jalview/datamodel/HiddenSequences.java | 280 ++
src/jalview/datamodel/Mapping.java | 455 ++
src/jalview/datamodel/NodeTransformI.java | 27 +
src/jalview/datamodel/PDBEntry.java | 112 +
src/jalview/datamodel/Provenance.java | 47 +
src/jalview/datamodel/ProvenanceEntry.java | 53 +
src/jalview/datamodel/SearchResults.java | 190 +
src/jalview/datamodel/SeqCigar.java | 770 +++
src/jalview/datamodel/Sequence.java | 1175 +++++
src/jalview/datamodel/SequenceFeature.java | 299 ++
src/jalview/datamodel/SequenceGroup.java | 1170 +++++
src/jalview/datamodel/SequenceI.java | 352 ++
src/jalview/datamodel/SequenceNode.java | 184 +
src/jalview/datamodel/SequencePoint.java | 50 +
src/jalview/datamodel/UniprotEntry.java | 97 +
src/jalview/datamodel/UniprotFile.java | 35 +
src/jalview/datamodel/UniprotProteinName.java | 37 +
src/jalview/datamodel/UniprotSequence.java | 45 +
src/jalview/datamodel/xdb/embl/BasePosition.java | 59 +
src/jalview/datamodel/xdb/embl/EmblEntry.java | 823 ++++
src/jalview/datamodel/xdb/embl/EmblError.java | 40 +
src/jalview/datamodel/xdb/embl/EmblFeature.java | 100 +
.../datamodel/xdb/embl/EmblFeatureLocElement.java | 116 +
.../datamodel/xdb/embl/EmblFeatureLocations.java | 168 +
src/jalview/datamodel/xdb/embl/EmblFile.java | 143 +
src/jalview/datamodel/xdb/embl/EmblSequence.java | 78 +
src/jalview/datamodel/xdb/embl/Qualifier.java | 108 +
src/jalview/ext/jmol/JalviewJmolBinding.java | 1546 ++++++
src/jalview/ext/jmol/JmolCommands.java | 166 +
src/jalview/gui/AlignFrame.java | 5109 ++++++++++++++++++++
src/jalview/gui/AlignViewport.java | 2285 +++++++++
src/jalview/gui/AlignmentPanel.java | 1453 ++++++
src/jalview/gui/AnnotationColourChooser.java | 579 +++
src/jalview/gui/AnnotationExporter.java | 303 ++
src/jalview/gui/AnnotationLabels.java | 878 ++++
src/jalview/gui/AnnotationPanel.java | 1503 ++++++
src/jalview/gui/AppJmol.java | 1331 +++++
src/jalview/gui/AppJmolBinding.java | 230 +
src/jalview/gui/AssociatePdbFileWithSeq.java | 78 +
src/jalview/gui/BlogReader.java | 851 ++++
src/jalview/gui/ConservationThread.java | 103 +
src/jalview/gui/Console.java | 649 +++
src/jalview/gui/CutAndPasteTransfer.java | 260 +
src/jalview/gui/DasSourceBrowser.java | 962 ++++
src/jalview/gui/Desktop.java | 2504 ++++++++++
src/jalview/gui/EPSOptions.java | 148 +
src/jalview/gui/EditNameDialog.java | 82 +
src/jalview/gui/FeatureColourChooser.java | 545 +++
src/jalview/gui/FeatureRenderer.java | 1462 ++++++
src/jalview/gui/FeatureSettings.java | 1741 +++++++
src/jalview/gui/Finder.java | 264 +
src/jalview/gui/FontChooser.java | 270 ++
src/jalview/gui/IProgressIndicator.java | 49 +
src/jalview/gui/IProgressIndicatorHandler.java | 35 +
src/jalview/gui/IdCanvas.java | 488 ++
src/jalview/gui/IdPanel.java | 514 ++
src/jalview/gui/IdwidthAdjuster.java | 171 +
src/jalview/gui/Jalview2XML.java | 3917 +++++++++++++++
src/jalview/gui/Jalview2XML_V1.java | 468 ++
src/jalview/gui/JalviewAppender.java | 60 +
src/jalview/gui/JalviewChangeSupport.java | 87 +
src/jalview/gui/JalviewDialog.java | 171 +
src/jalview/gui/JvSwingUtils.java | 194 +
src/jalview/gui/OOMWarning.java | 88 +
src/jalview/gui/OptsAndParamsPage.java | 883 ++++
src/jalview/gui/OptsParametersContainerI.java | 30 +
src/jalview/gui/OverviewPanel.java | 458 ++
src/jalview/gui/PCAPanel.java | 588 +++
src/jalview/gui/PaintRefresher.java | 245 +
src/jalview/gui/PairwiseAlignPanel.java | 154 +
src/jalview/gui/PopupMenu.java | 1897 ++++++++
src/jalview/gui/Preferences.java | 678 +++
src/jalview/gui/PromptUserConfig.java | 249 +
src/jalview/gui/RedundancyPanel.java | 341 ++
src/jalview/gui/RestInputParamEditDialog.java | 266 +
src/jalview/gui/RestServiceEditorPane.java | 506 ++
src/jalview/gui/RotatableCanvas.java | 835 ++++
src/jalview/gui/ScalePanel.java | 511 ++
src/jalview/gui/ScriptWindow.java | 732 +++
src/jalview/gui/SeqCanvas.java | 946 ++++
src/jalview/gui/SeqPanel.java | 1970 ++++++++
src/jalview/gui/SequenceFetcher.java | 834 ++++
src/jalview/gui/SequenceRenderer.java | 494 ++
src/jalview/gui/SliderPanel.java | 372 ++
src/jalview/gui/SplashScreen.java | 221 +
src/jalview/gui/TextColourChooser.java | 207 +
src/jalview/gui/TreeCanvas.java | 995 ++++
src/jalview/gui/TreePanel.java | 830 ++++
src/jalview/gui/UserDefinedColours.java | 932 ++++
src/jalview/gui/UserQuestionnaireCheck.java | 158 +
src/jalview/gui/VamsasApplication.java | 1114 +++++
src/jalview/gui/ViewSelectionMenu.java | 308 ++
src/jalview/gui/WebserviceInfo.java | 842 ++++
src/jalview/gui/WsJobParameters.java | 1388 ++++++
src/jalview/gui/WsParamSetManager.java | 315 ++
src/jalview/gui/WsPreferences.java | 525 ++
src/jalview/io/AMSAFile.java | 102 +
src/jalview/io/AlignFile.java | 290 ++
src/jalview/io/AlignmentProperties.java | 147 +
src/jalview/io/AnnotationFile.java | 1487 ++++++
src/jalview/io/AppletFormatAdapter.java | 718 +++
src/jalview/io/BLCFile.java | 282 ++
src/jalview/io/ClansFile.java | 27 +
src/jalview/io/ClustalFile.java | 219 +
src/jalview/io/DBRefFile.java | 44 +
src/jalview/io/FastaFile.java | 241 +
src/jalview/io/FeaturesFile.java | 1002 ++++
src/jalview/io/FileLoader.java | 463 ++
src/jalview/io/FileParse.java | 410 ++
src/jalview/io/FormatAdapter.java | 245 +
src/jalview/io/HTMLOutput.java | 381 ++
src/jalview/io/IdentifyFile.java | 300 ++
src/jalview/io/JPredFile.java | 431 ++
src/jalview/io/JalviewFileChooser.java | 286 ++
src/jalview/io/JalviewFileFilter.java | 172 +
src/jalview/io/JalviewFileView.java | 110 +
src/jalview/io/JnetAnnotationMaker.java | 200 +
src/jalview/io/MSFfile.java | 414 ++
src/jalview/io/MatrixFile.java | 34 +
src/jalview/io/ModellerDescription.java | 421 ++
src/jalview/io/NewickFile.java | 975 ++++
src/jalview/io/PIRFile.java | 198 +
src/jalview/io/PfamFile.java | 177 +
src/jalview/io/PileUpfile.java | 200 +
src/jalview/io/SimpleBlastFile.java | 294 ++
src/jalview/io/StockholmFile.java | 583 +++
src/jalview/io/VamsasAppDatastore.java | 2778 +++++++++++
src/jalview/io/WSWUBlastClient.java | 304 ++
src/jalview/io/packed/DataProvider.java | 78 +
src/jalview/io/packed/JalviewDataset.java | 272 ++
src/jalview/io/packed/ParsePackedSet.java | 297 ++
src/jalview/io/packed/SimpleDataProvider.java | 66 +
src/jalview/io/vamsas/Datasetsequence.java | 275 ++
src/jalview/io/vamsas/DatastoreItem.java | 582 +++
src/jalview/io/vamsas/DatastoreRegistry.java | 176 +
src/jalview/io/vamsas/Dbref.java | 236 +
src/jalview/io/vamsas/LocalDocSyncObject.java | 124 +
src/jalview/io/vamsas/Rangetype.java | 336 ++
src/jalview/io/vamsas/Sequencefeature.java | 359 ++
src/jalview/io/vamsas/Sequencemapping.java | 465 ++
src/jalview/io/vamsas/Tree.java | 643 +++
src/jalview/javascript/JSFunctionExec.java | 273 ++
src/jalview/javascript/JalviewLiteJsApi.java | 511 ++
src/jalview/javascript/JsCallBack.java | 25 +
src/jalview/javascript/JsSelectionSender.java | 147 +
src/jalview/javascript/MouseOverListener.java | 101 +
.../javascript/MouseOverStructureListener.java | 322 ++
src/jalview/jbgui/GAlignFrame.java | 2420 +++++++++
src/jalview/jbgui/GAlignmentPanel.java | 125 +
src/jalview/jbgui/GCutAndPasteTransfer.java | 233 +
src/jalview/jbgui/GDasSourceBrowser.java | 221 +
src/jalview/jbgui/GDesktop.java | 528 ++
src/jalview/jbgui/GFinder.java | 197 +
src/jalview/jbgui/GFontChooser.java | 275 ++
src/jalview/jbgui/GPCAPanel.java | 306 ++
src/jalview/jbgui/GPairwiseAlignPanel.java | 93 +
src/jalview/jbgui/GPreferences.java | 896 ++++
src/jalview/jbgui/GRestInputParamEditDialog.java | 110 +
src/jalview/jbgui/GRestServiceEditorPane.java | 517 ++
src/jalview/jbgui/GSequenceLink.java | 158 +
src/jalview/jbgui/GSliderPanel.java | 207 +
src/jalview/jbgui/GStructureViewer.java | 398 ++
src/jalview/jbgui/GTreePanel.java | 278 ++
src/jalview/jbgui/GUserDefinedColours.java | 283 ++
src/jalview/jbgui/GWebserviceInfo.java | 124 +
src/jalview/jbgui/GWsPreferences.java | 499 ++
src/jalview/math/Matrix.java | 856 ++++
src/jalview/math/RotatableMatrix.java | 343 ++
src/jalview/schemabinding/version2/.castor.cdr | 45 +
src/jalview/schemabinding/version2/AlcodMap.java | 201 +
src/jalview/schemabinding/version2/Alcodon.java | 280 ++
.../schemabinding/version2/AlcodonFrame.java | 449 ++
src/jalview/schemabinding/version2/Annotation.java | 1102 +++++
.../schemabinding/version2/AnnotationColours.java | 379 ++
.../schemabinding/version2/AnnotationElement.java | 357 ++
src/jalview/schemabinding/version2/Colour.java | 500 ++
src/jalview/schemabinding/version2/DBRef.java | 236 +
src/jalview/schemabinding/version2/Feature.java | 536 ++
.../schemabinding/version2/FeatureSettings.java | 449 ++
src/jalview/schemabinding/version2/Features.java | 133 +
src/jalview/schemabinding/version2/Group.java | 219 +
.../schemabinding/version2/HiddenColumns.java | 233 +
src/jalview/schemabinding/version2/JGroup.java | 1167 +++++
src/jalview/schemabinding/version2/JSeq.java | 831 ++++
.../schemabinding/version2/JalviewModel.java | 238 +
.../version2/JalviewModelSequence.java | 942 ++++
.../schemabinding/version2/JalviewUserColours.java | 348 ++
.../schemabinding/version2/MapListFrom.java | 233 +
src/jalview/schemabinding/version2/MapListTo.java | 233 +
.../schemabinding/version2/MapListType.java | 599 +++
src/jalview/schemabinding/version2/Mapping.java | 182 +
.../schemabinding/version2/MappingChoice.java | 187 +
src/jalview/schemabinding/version2/OtherData.java | 187 +
src/jalview/schemabinding/version2/Pdbentry.java | 369 ++
.../schemabinding/version2/PdbentryItem.java | 209 +
src/jalview/schemabinding/version2/Pdbids.java | 297 ++
src/jalview/schemabinding/version2/Property.java | 187 +
src/jalview/schemabinding/version2/Sequence.java | 328 ++
.../schemabinding/version2/SequenceSet.java | 824 ++++
.../version2/SequenceSetProperties.java | 187 +
.../schemabinding/version2/SequenceType.java | 237 +
src/jalview/schemabinding/version2/Setting.java | 683 +++
.../schemabinding/version2/StructureState.java | 693 +++
.../schemabinding/version2/ThresholdLine.java | 258 +
src/jalview/schemabinding/version2/Tree.java | 869 ++++
.../schemabinding/version2/UserColourScheme.java | 134 +
.../schemabinding/version2/UserColours.java | 187 +
src/jalview/schemabinding/version2/VAMSAS.java | 446 ++
.../schemabinding/version2/VamsasModel.java | 133 +
src/jalview/schemabinding/version2/Viewport.java | 2451 ++++++++++
.../version2/WebServiceParameterSet.java | 456 ++
.../version2/descriptors/AlcodMapDescriptor.java | 251 +
.../version2/descriptors/AlcodonDescriptor.java | 297 ++
.../descriptors/AlcodonFrameDescriptor.java | 261 +
.../descriptors/AnnotationColoursDescriptor.java | 420 ++
.../version2/descriptors/AnnotationDescriptor.java | 943 ++++
.../descriptors/AnnotationElementDescriptor.java | 422 ++
.../version2/descriptors/ColourDescriptor.java | 534 ++
.../version2/descriptors/DBRefDescriptor.java | 321 ++
.../version2/descriptors/FeatureDescriptor.java | 498 ++
.../descriptors/FeatureSettingsDescriptor.java | 261 +
.../version2/descriptors/FeaturesDescriptor.java | 168 +
.../version2/descriptors/GroupDescriptor.java | 254 +
.../descriptors/HiddenColumnsDescriptor.java | 260 +
.../version2/descriptors/JGroupDescriptor.java | 967 ++++
.../version2/descriptors/JSeqDescriptor.java | 520 ++
.../descriptors/JalviewModelDescriptor.java | 329 ++
.../JalviewModelSequenceDescriptor.java | 421 ++
.../descriptors/JalviewUserColoursDescriptor.java | 293 ++
.../descriptors/MapListFromDescriptor.java | 260 +
.../version2/descriptors/MapListToDescriptor.java | 260 +
.../descriptors/MapListTypeDescriptor.java | 345 ++
.../descriptors/MappingChoiceDescriptor.java | 247 +
.../version2/descriptors/MappingDescriptor.java | 213 +
.../version2/descriptors/OtherDataDescriptor.java | 252 +
.../version2/descriptors/PdbentryDescriptor.java | 329 ++
.../descriptors/PdbentryItemDescriptor.java | 219 +
.../version2/descriptors/PdbidsDescriptor.java | 220 +
.../version2/descriptors/PropertyDescriptor.java | 252 +
.../version2/descriptors/SequenceDescriptor.java | 257 +
.../descriptors/SequenceSetDescriptor.java | 421 ++
.../SequenceSetPropertiesDescriptor.java | 248 +
.../descriptors/SequenceTypeDescriptor.java | 327 ++
.../version2/descriptors/SettingDescriptor.java | 637 +++
.../descriptors/StructureStateDescriptor.java | 583 +++
.../descriptors/ThresholdLineDescriptor.java | 297 ++
.../version2/descriptors/TreeDescriptor.java | 832 ++++
.../descriptors/UserColourSchemeDescriptor.java | 168 +
.../descriptors/UserColoursDescriptor.java | 249 +
.../version2/descriptors/VAMSASDescriptor.java | 266 +
.../descriptors/VamsasModelDescriptor.java | 168 +
.../version2/descriptors/ViewportDescriptor.java | 1975 ++++++++
.../WebServiceParameterSetDescriptor.java | 371 ++
src/jalview/schemes/AnnotationColourGradient.java | 226 +
src/jalview/schemes/Blosum62ColourScheme.java | 88 +
src/jalview/schemes/BuriedColourScheme.java | 51 +
src/jalview/schemes/ClustalxColourScheme.java | 334 ++
src/jalview/schemes/ColourSchemeI.java | 42 +
src/jalview/schemes/ColourSchemeProperty.java | 525 ++
src/jalview/schemes/Consensus.java | 94 +
src/jalview/schemes/GraduatedColor.java | 295 ++
src/jalview/schemes/HelixColourScheme.java | 34 +
src/jalview/schemes/HydrophobicColourScheme.java | 51 +
src/jalview/schemes/NucleotideColourScheme.java | 87 +
src/jalview/schemes/PIDColourScheme.java | 92 +
src/jalview/schemes/ResidueColourScheme.java | 281 ++
src/jalview/schemes/ResidueProperties.java | 1310 +++++
src/jalview/schemes/ScoreColourScheme.java | 125 +
src/jalview/schemes/ScoreMatrix.java | 86 +
src/jalview/schemes/StrandColourScheme.java | 51 +
src/jalview/schemes/TaylorColourScheme.java | 26 +
src/jalview/schemes/TurnColourScheme.java | 51 +
src/jalview/schemes/UserColourScheme.java | 238 +
src/jalview/schemes/ZappoColourScheme.java | 35 +
.../structure/AlignmentViewPanelListener.java | 33 +
src/jalview/structure/SelectionListener.java | 39 +
src/jalview/structure/SelectionSource.java | 28 +
src/jalview/structure/SequenceListener.java | 29 +
src/jalview/structure/StructureListener.java | 68 +
src/jalview/structure/StructureMapping.java | 98 +
.../structure/StructureMappingcommandSet.java | 51 +
.../structure/StructureSelectionManager.java | 813 ++++
src/jalview/structure/VamsasListener.java | 34 +
src/jalview/structure/VamsasSource.java | 31 +
src/jalview/util/AWTConsole.java | 249 +
src/jalview/util/BrowserLauncher.java | 889 ++++
src/jalview/util/Comparison.java | 259 +
src/jalview/util/DBRefUtils.java | 449 ++
src/jalview/util/Format.java | 938 ++++
src/jalview/util/GroupUrlLink.java | 911 ++++
src/jalview/util/ImageMaker.java | 185 +
src/jalview/util/MapList.java | 1000 ++++
src/jalview/util/ParseHtmlBodyAndLinks.java | 156 +
src/jalview/util/Platform.java | 54 +
src/jalview/util/QuickSort.java | 229 +
src/jalview/util/ShiftList.java | 143 +
src/jalview/util/TableSorter.java | 597 +++
src/jalview/util/UrlLink.java | 398 ++
src/jalview/util/jarInputStreamProvider.java | 45 +
src/jalview/ws/AWSThread.java | 369 ++
src/jalview/ws/AWsJob.java | 227 +
src/jalview/ws/DBRefFetcher.java | 721 +++
src/jalview/ws/DasSequenceFeatureFetcher.java | 898 ++++
src/jalview/ws/EnfinEnvision2OneWay.java | 709 +++
src/jalview/ws/JobStateSummary.java | 165 +
src/jalview/ws/SequenceFetcher.java | 407 ++
src/jalview/ws/WSClient.java | 74 +
src/jalview/ws/WSClientI.java | 46 +
src/jalview/ws/WSMenuEntryProviderI.java | 36 +
src/jalview/ws/dbsources/DasSequenceSource.java | 176 +
.../ws/dbsources/EbiFileRetrievedProxy.java | 64 +
src/jalview/ws/dbsources/EmblCdsSouce.java | 88 +
src/jalview/ws/dbsources/EmblSource.java | 127 +
src/jalview/ws/dbsources/EmblXmlSource.java | 162 +
src/jalview/ws/dbsources/GeneDbSource.java | 130 +
src/jalview/ws/dbsources/Pdb.java | 218 +
src/jalview/ws/dbsources/Pfam.java | 154 +
src/jalview/ws/dbsources/PfamFull.java | 63 +
src/jalview/ws/dbsources/PfamSeed.java | 65 +
src/jalview/ws/dbsources/Uniprot.java | 297 ++
src/jalview/ws/dbsources/UnprotName.java | 41 +
.../dbsources/das/DasSequenceSourceListener.java | 165 +
src/jalview/ws/ebi/EBIFetchClient.java | 242 +
src/jalview/ws/io/mime/HttpContentHandler.java | 34 +
.../ws/io/mime/JalviewMimeContentHandler.java | 173 +
src/jalview/ws/io/mime/MimeTypes.java | 78 +
src/jalview/ws/jws1/Discoverer.java | 433 ++
src/jalview/ws/jws1/JPredClient.java | 354 ++
src/jalview/ws/jws1/JPredThread.java | 574 +++
src/jalview/ws/jws1/JWS1Thread.java | 48 +
src/jalview/ws/jws1/MsaWSClient.java | 235 +
src/jalview/ws/jws1/MsaWSThread.java | 702 +++
src/jalview/ws/jws1/SeqSearchWSClient.java | 316 ++
src/jalview/ws/jws1/SeqSearchWSThread.java | 661 +++
src/jalview/ws/jws1/WS1Client.java | 129 +
src/jalview/ws/jws1/WSJob.java | 147 +
src/jalview/ws/jws2/AWS2Thread.java | 33 +
src/jalview/ws/jws2/JWs2Job.java | 158 +
src/jalview/ws/jws2/JabaParamStore.java | 338 ++
src/jalview/ws/jws2/JabaPreset.java | 97 +
src/jalview/ws/jws2/JabaWsServerQuery.java | 128 +
src/jalview/ws/jws2/Jws2Client.java | 70 +
src/jalview/ws/jws2/Jws2Discoverer.java | 804 +++
src/jalview/ws/jws2/MsaWSClient.java | 365 ++
src/jalview/ws/jws2/MsaWSThread.java | 975 ++++
src/jalview/ws/jws2/ParameterUtils.java | 205 +
src/jalview/ws/jws2/dm/JabaOption.java | 105 +
src/jalview/ws/jws2/dm/JabaParameter.java | 55 +
src/jalview/ws/jws2/dm/JabaValueConstrain.java | 59 +
src/jalview/ws/jws2/dm/JabaWsParamSet.java | 204 +
src/jalview/ws/params/ArgumentI.java | 40 +
.../ws/params/InvalidArgumentException.java | 50 +
src/jalview/ws/params/OptionI.java | 36 +
src/jalview/ws/params/ParamDatastoreI.java | 89 +
src/jalview/ws/params/ParamManager.java | 71 +
src/jalview/ws/params/ParameterI.java | 31 +
src/jalview/ws/params/ValueConstrainI.java | 40 +
src/jalview/ws/params/WsParamSetI.java | 80 +
src/jalview/ws/params/simple/BooleanOption.java | 35 +
src/jalview/ws/params/simple/IntegerParameter.java | 99 +
src/jalview/ws/params/simple/Option.java | 118 +
src/jalview/ws/params/simple/Parameter.java | 42 +
.../ws/params/simple/StringChoiceParameter.java | 23 +
src/jalview/ws/rest/AlignmentProcessor.java | 29 +
src/jalview/ws/rest/HttpResultSet.java | 232 +
src/jalview/ws/rest/InputType.java | 266 +
src/jalview/ws/rest/NoValidInputDataException.java | 38 +
src/jalview/ws/rest/RestClient.java | 451 ++
src/jalview/ws/rest/RestJob.java | 473 ++
src/jalview/ws/rest/RestJobThread.java | 1311 +++++
src/jalview/ws/rest/RestServiceDescription.java | 1096 +++++
src/jalview/ws/rest/params/Alignment.java | 205 +
src/jalview/ws/rest/params/AnnotationFile.java | 124 +
src/jalview/ws/rest/params/JobConstant.java | 115 +
.../ws/rest/params/SeqGroupIndexVector.java | 302 ++
src/jalview/ws/rest/params/SeqIdVector.java | 138 +
src/jalview/ws/rest/params/SeqVector.java | 128 +
src/jalview/ws/rest/params/Tree.java | 81 +
src/jalview/ws/seqfetcher/ASequenceFetcher.java | 334 ++
src/jalview/ws/seqfetcher/DbSourceProxy.java | 131 +
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 139 +
.../biojava/dasobert/das/DAS_FeatureRetrieve.java | 287 ++
.../biojava/dasobert/das/DAS_Feature_Handler.java | 314 ++
.../biojava/dasobert/das/DAS_Sequence_Handler.java | 161 +
src/org/biojava/dasobert/das/FeatureThread.java | 198 +
src/org/biojava/dasobert/das/SequenceThread.java | 299 ++
src/org/biojava/dasobert/das2/Das2Capability.java | 51 +
.../biojava/dasobert/das2/Das2CapabilityImpl.java | 131 +
src/org/biojava/dasobert/das2/Das2Source.java | 42 +
src/org/biojava/dasobert/das2/Das2SourceImpl.java | 157 +
.../biojava/dasobert/das2/DasSourceConverter.java | 92 +
.../dasobert/das2/io/DAS2SourceHandler.java | 216 +
.../biojava/dasobert/das2/io/DasSourceReader.java | 33 +
.../dasobert/das2/io/DasSourceReaderImpl.java | 183 +
.../biojava/dasobert/dasregistry/Das1Source.java | 305 ++
.../dasobert/dasregistry/Das2Validator.java | 44 +
.../dasregistry/DasCoordSysComparator.java | 128 +
.../dasobert/dasregistry/DasCoordinateSystem.java | 233 +
.../biojava/dasobert/dasregistry/DasSource.java | 130 +
.../dasobert/dasregistry/DasSourceComparator.java | 190 +
.../dasobert/eventmodel/AbstractDasEvent.java | 43 +
.../biojava/dasobert/eventmodel/FeatureEvent.java | 96 +
.../dasobert/eventmodel/FeatureListener.java | 48 +
.../dasobert/eventmodel/ObjectListener.java | 51 +
.../biojava/dasobert/eventmodel/SequenceEvent.java | 62 +
.../dasobert/eventmodel/SequenceListener.java | 64 +
.../dasobert/feature/AbstractFeatureTrack.java | 278 ++
.../biojava/dasobert/feature/AbstractSegment.java | 256 +
.../dasobert/feature/FeatureComparator.java | 87 +
.../dasobert/feature/FeatureMapComparator.java | 68 +
src/org/biojava/dasobert/feature/FeatureTrack.java | 127 +
.../dasobert/feature/FeatureTrackConverter.java | 526 ++
.../biojava/dasobert/feature/FeatureTrackImpl.java | 68 +
.../biojava/dasobert/feature/HistogramFeature.java | 95 +
.../biojava/dasobert/feature/HistogramSegment.java | 67 +
src/org/biojava/dasobert/feature/Segment.java | 84 +
.../dasobert/feature/SegmentComparator.java | 45 +
src/org/biojava/dasobert/feature/SegmentImpl.java | 83 +
src/org/jibble/epsgraphics/EpsDocument.java | 267 +
src/org/jibble/epsgraphics/EpsException.java | 27 +
src/org/jibble/epsgraphics/EpsGraphics2D.java | 1444 ++++++
src/uk/ac/ebi/picr/model/CrossReference.java | 330 ++
.../ac/ebi/picr/model/CrossReference_Helper.java | 125 +
src/uk/ac/ebi/picr/model/UPEntry.java | 290 ++
src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 106 +
src/uk/ac/ebi/www/Data.java | 154 +
src/uk/ac/ebi/www/InputParams.java | 466 ++
src/uk/ac/ebi/www/WSFile.java | 154 +
src/uk/ac/ebi/www/WSWUBlast.java | 42 +
src/uk/ac/ebi/www/WSWUBlastService.java | 29 +
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 132 +
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 487 ++
.../AccessionMapperBindingStub.java | 397 ++
.../AccessionMapperInterface.java | 34 +
.../AccessionMapperService.java | 29 +
.../AccessionMapperServiceLocator.java | 189 +
src/vamsas/IMsaWS.java | 31 +
src/vamsas/objects/simple/Alignment.java | 162 +
src/vamsas/objects/simple/Alignment_Helper.java | 80 +
src/vamsas/objects/simple/JpredResult.java | 131 +
src/vamsas/objects/simple/JpredResult_Helper.java | 74 +
src/vamsas/objects/simple/MsaResult.java | 131 +
src/vamsas/objects/simple/MsaResult_Helper.java | 86 +
src/vamsas/objects/simple/Msfalignment.java | 130 +
src/vamsas/objects/simple/Msfalignment_Helper.java | 74 +
src/vamsas/objects/simple/Object.java | 63 +
src/vamsas/objects/simple/Object_Helper.java | 62 +
src/vamsas/objects/simple/Result.java | 349 ++
src/vamsas/objects/simple/Result_Helper.java | 128 +
src/vamsas/objects/simple/Secstructpred.java | 100 +
.../objects/simple/Secstructpred_Helper.java | 68 +
src/vamsas/objects/simple/SeqSearchResult.java | 185 +
.../objects/simple/SeqSearchResult_Helper.java | 86 +
src/vamsas/objects/simple/Sequence.java | 124 +
src/vamsas/objects/simple/SequenceSet.java | 101 +
src/vamsas/objects/simple/SequenceSet_Helper.java | 68 +
src/vamsas/objects/simple/Sequence_Helper.java | 74 +
src/vamsas/objects/simple/WsJobId.java | 120 +
src/vamsas/objects/simple/WsJobId_Helper.java | 74 +
864 files changed, 262978 insertions(+)
--
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