source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	darolmar <darolmar@gmail.com>
	Tue, 23 Sep 2014 14:34:33 +0000 (16:34 +0200)
committer	darolmar <darolmar@gmail.com>
	Tue, 23 Sep 2014 14:34:33 +0000 (16:34 +0200)
commit	aced09c4feeaf3406269442c14e54abeeb4cad81
tree	3d24348104d915815d3c678ef08678afabeda52e	tree \| snapshot
parent	5d32c7ad007e098894b332b6fca61e1824972c50	commit \| diff

JAL-1355

165 files changed:

resources/lang/Messages.properties		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/com/stevesoft/pat/Pattern.java		diff \| blob \| history
src/com/stevesoft/pat/Regex.java		diff \| blob \| history
src/com/stevesoft/pat/Replacer.java		diff \| blob \| history
src/com/stevesoft/pat/Transformer.java		diff \| blob \| history
src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java		diff \| blob \| history
src/ext/vamsas/IRegistryServiceLocator.java		diff \| blob \| history
src/ext/vamsas/JpredServiceLocator.java		diff \| blob \| history
src/ext/vamsas/MuscleWSServiceLocator.java		diff \| blob \| history
src/ext/vamsas/SeqSearchServiceLocator.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/Rna.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AppletJmol.java		diff \| blob \| history
src/jalview/appletgui/EmbmenuFrame.java		diff \| blob \| history
src/jalview/appletgui/FeatureRenderer.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/binding/Annotation.java		diff \| blob \| history
src/jalview/binding/FeatureSettings.java		diff \| blob \| history
src/jalview/binding/JGroup.java		diff \| blob \| history
src/jalview/binding/JSeq.java		diff \| blob \| history
src/jalview/binding/JalviewModelSequence.java		diff \| blob \| history
src/jalview/binding/JalviewUserColours.java		diff \| blob \| history
src/jalview/binding/Pdbentry.java		diff \| blob \| history
src/jalview/binding/PdbentryItem.java		diff \| blob \| history
src/jalview/binding/SequenceSet.java		diff \| blob \| history
src/jalview/binding/VAMSAS.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentOrder.java		diff \| blob \| history
src/jalview/datamodel/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/CigarBase.java		diff \| blob \| history
src/jalview/datamodel/SeqCigar.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/jmol/PDBFileWithJmol.java		diff \| blob \| history
src/jalview/ext/paradise/Annotate3D.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/BlogReader.java		diff \| blob \| history
src/jalview/gui/ChimeraViewFrame.java		diff \| blob \| history
src/jalview/gui/Console.java		diff \| blob \| history
src/jalview/gui/CutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/JDatabaseTree.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/OOMWarning.java		diff \| blob \| history
src/jalview/gui/OptsAndParamsPage.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/TextColourChooser.java		diff \| blob \| history
src/jalview/gui/TreeCanvas.java		diff \| blob \| history
src/jalview/gui/TreePanel.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/gui/VamsasApplication.java		diff \| blob \| history
src/jalview/gui/WebserviceInfo.java		diff \| blob \| history
src/jalview/gui/WsJobParameters.java		diff \| blob \| history
src/jalview/gui/WsParamSetManager.java		diff \| blob \| history
src/jalview/gui/WsPreferences.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java		diff \| blob \| history
src/jalview/io/JPredFile.java		diff \| blob \| history
src/jalview/io/JalviewFileChooser.java		diff \| blob \| history
src/jalview/io/JnetAnnotationMaker.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/RnamlFile.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/io/vamsas/DatastoreItem.java		diff \| blob \| history
src/jalview/io/vamsas/Rangetype.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GSequenceLink.java		diff \| blob \| history
src/jalview/math/Matrix.java		diff \| blob \| history
src/jalview/schemabinding/version2/AlcodonFrame.java		diff \| blob \| history
src/jalview/schemabinding/version2/Annotation.java		diff \| blob \| history
src/jalview/schemabinding/version2/Feature.java		diff \| blob \| history
src/jalview/schemabinding/version2/FeatureSettings.java		diff \| blob \| history
src/jalview/schemabinding/version2/JGroup.java		diff \| blob \| history
src/jalview/schemabinding/version2/JSeq.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewModelSequence.java		diff \| blob \| history
src/jalview/schemabinding/version2/JalviewUserColours.java		diff \| blob \| history
src/jalview/schemabinding/version2/MapListType.java		diff \| blob \| history
src/jalview/schemabinding/version2/Pdbentry.java		diff \| blob \| history
src/jalview/schemabinding/version2/PdbentryItem.java		diff \| blob \| history
src/jalview/schemabinding/version2/Pdbids.java		diff \| blob \| history
src/jalview/schemabinding/version2/Sequence.java		diff \| blob \| history
src/jalview/schemabinding/version2/SequenceSet.java		diff \| blob \| history
src/jalview/schemabinding/version2/VAMSAS.java		diff \| blob \| history
src/jalview/schemabinding/version2/Viewport.java		diff \| blob \| history
src/jalview/schemabinding/version2/WebServiceParameterSet.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/util/AWTConsole.java		diff \| blob \| history
src/jalview/util/BrowserLauncher.java		diff \| blob \| history
src/jalview/util/GroupUrlLink.java		diff \| blob \| history
src/jalview/ws/AWSThread.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/DasSequenceFeatureFetcher.java		diff \| blob \| history
src/jalview/ws/EnfinEnvision2OneWay.java		diff \| blob \| history
src/jalview/ws/dbsources/EmblXmlSource.java		diff \| blob \| history
src/jalview/ws/dbsources/Pdb.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java		diff \| blob \| history
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java		diff \| blob \| history
src/jalview/ws/ebi/EBIFetchClient.java		diff \| blob \| history
src/jalview/ws/jws1/Annotate3D.java		diff \| blob \| history
src/jalview/ws/jws1/JPredClient.java		diff \| blob \| history
src/jalview/ws/jws1/JPredThread.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSClient.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSThread.java		diff \| blob \| history
src/jalview/ws/jws1/WS1Client.java		diff \| blob \| history
src/jalview/ws/jws2/JabaParamStore.java		diff \| blob \| history
src/jalview/ws/jws2/JabaPreset.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/jws2/ParameterUtils.java		diff \| blob \| history
src/jalview/ws/jws2/SequenceAnnotationWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/dm/AAConSettings.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaOption.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaValueConstrain.java		diff \| blob \| history
src/jalview/ws/jws2/dm/JabaWsParamSet.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2Instance.java		diff \| blob \| history
src/jalview/ws/rest/HttpResultSet.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/rest/RestJobThread.java		diff \| blob \| history
src/jalview/ws/rest/params/JobConstant.java		diff \| blob \| history
src/jalview/ws/rest/params/SeqGroupIndexVector.java		diff \| blob \| history
src/jalview/ws/rest/params/Tree.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/org/jibble/epsgraphics/EpsDocument.java		diff \| blob \| history
src/org/jibble/epsgraphics/EpsGraphics2D.java		diff \| blob \| history
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java		diff \| blob \| history
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java		diff \| blob \| history

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