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 <[email protected]> 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(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/jalview.git _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
