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

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

author	jprocter <Jim Procter>
	Sun, 10 Sep 2006 12:48:27 +0000 (12:48 +0000)
committer	jprocter <Jim Procter>
	Sun, 10 Sep 2006 12:48:27 +0000 (12:48 +0000)
commit	e894eb87d40be6e8452d19032ddffe80dad5f804
tree	9b5e512cde2240e03f16596eaa9ba4271b76ff13	tree \| snapshot
parent	0f71bfca98457c30f1051f142c31b6aaa3e23ead	commit \| diff

updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

198 files changed:

src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/AppletPDBViewer.java		diff \| blob \| history
src/MCview/Atom.java		diff \| blob \| history
src/MCview/Bond.java		diff \| blob \| history
src/MCview/MCMatrix.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/MCview/PDBChain.java		diff \| blob \| history
src/MCview/PDBViewer.java		diff \| blob \| history
src/MCview/PDBfile.java		diff \| blob \| history
src/MCview/Residue.java		diff \| blob \| history
src/MCview/Zsort.java		diff \| blob \| history
src/ext/vamsas/MuscleWS.java		diff \| blob \| history
src/ext/vamsas/MuscleWSService.java		diff \| blob \| history
src/ext/vamsas/MuscleWSServiceLocator.java		diff \| blob \| history
src/ext/vamsas/MuscleWSSoapBindingStub.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentSorter.java		diff \| blob \| history
src/jalview/analysis/Conservation.java		diff \| blob \| history
src/jalview/analysis/NJTree.java		diff \| blob \| history
src/jalview/analysis/PCA.java		diff \| blob \| history
src/jalview/analysis/SeqsetUtils.java		diff \| blob \| history
src/jalview/analysis/SequenceIdMatcher.java		diff \| blob \| history
src/jalview/appletgui/APopupMenu.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignViewport.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/appletgui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/appletgui/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/ColumnSelection.java	[deleted file]	blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/appletgui/FeatureRenderer.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/Finder.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/IdCanvas.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/PCAPanel.java		diff \| blob \| history
src/jalview/appletgui/PaintRefresher.java		diff \| blob \| history
src/jalview/appletgui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/appletgui/RedundancyPanel.java		diff \| blob \| history
src/jalview/appletgui/RotatableCanvas.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/SeqPanel.java		diff \| blob \| history
src/jalview/appletgui/SequenceRenderer.java		diff \| blob \| history
src/jalview/appletgui/SliderPanel.java		diff \| blob \| history
src/jalview/appletgui/TreeCanvas.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentAnnotation.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AlignmentOrder.java		diff \| blob \| history
src/jalview/datamodel/Annotation.java		diff \| blob \| history
src/jalview/datamodel/BinaryNode.java		diff \| blob \| history
src/jalview/datamodel/BinarySequence.java		diff \| blob \| history
src/jalview/datamodel/DBRefEntry.java		diff \| blob \| history
src/jalview/datamodel/GraphLine.java		diff \| blob \| history
src/jalview/datamodel/HiddenSequences.java		diff \| blob \| history
src/jalview/datamodel/HistoryItem.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/Provenance.java		diff \| blob \| history
src/jalview/datamodel/ProvenanceEntry.java		diff \| blob \| history
src/jalview/datamodel/SearchResults.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceFeature.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/datamodel/SequenceNode.java		diff \| blob \| history
src/jalview/datamodel/SequencePoint.java		diff \| blob \| history
src/jalview/datamodel/UniprotEntry.java		diff \| blob \| history
src/jalview/datamodel/UniprotFile.java		diff \| blob \| history
src/jalview/datamodel/UniprotSequence.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/ColumnSelection.java	[deleted file]	blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/EPSOptions.java		diff \| blob \| history
src/jalview/gui/FeatureRenderer.java		diff \| blob \| history
src/jalview/gui/FeatureSettings.java		diff \| blob \| history
src/jalview/gui/Finder.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/IdCanvas.java		diff \| blob \| history
src/jalview/gui/IdPanel.java		diff \| blob \| history
src/jalview/gui/IdwidthAdjuster.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PaintRefresher.java		diff \| blob \| history
src/jalview/gui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/Preferences.java		diff \| blob \| history
src/jalview/gui/RedundancyPanel.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/ScalePanel.java		diff \| blob \| history
src/jalview/gui/SeqCanvas.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SequenceRenderer.java		diff \| blob \| history
src/jalview/gui/SliderPanel.java		diff \| blob \| history
src/jalview/gui/SplashScreen.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/WebserviceInfo.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/AnnotationReader.java	[deleted file]	blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/BLCFile.java		diff \| blob \| history
src/jalview/io/ClustalFile.java		diff \| blob \| history
src/jalview/io/EBIFetchClient.java		diff \| blob \| history
src/jalview/io/FastaFile.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/FileParse.java		diff \| blob \| history
src/jalview/io/FormatAdapter.java		diff \| blob \| history
src/jalview/io/HTMLOutput.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/io/JPredFile.java		diff \| blob \| history
src/jalview/io/JalviewFileChooser.java		diff \| blob \| history
src/jalview/io/JalviewFileFilter.java		diff \| blob \| history
src/jalview/io/JalviewFileView.java		diff \| blob \| history
src/jalview/io/MSFfile.java		diff \| blob \| history
src/jalview/io/ModellerDescription.java		diff \| blob \| history
src/jalview/io/NewickFile.java		diff \| blob \| history
src/jalview/io/PIRFile.java		diff \| blob \| history
src/jalview/io/PfamFile.java		diff \| blob \| history
src/jalview/io/PileUpfile.java		diff \| blob \| history
src/jalview/io/SequenceFeatureFetcher.java	[deleted file]	blob \| history
src/jalview/io/VamsasDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GAlignmentPanel.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteTransfer.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GFinder.java		diff \| blob \| history
src/jalview/jbgui/GFontChooser.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPairwiseAlignPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GSequenceLink.java		diff \| blob \| history
src/jalview/jbgui/GSliderPanel.java		diff \| blob \| history
src/jalview/jbgui/GTreePanel.java		diff \| blob \| history
src/jalview/jbgui/GUserDefinedColours.java		diff \| blob \| history
src/jalview/jbgui/GWebserviceInfo.java		diff \| blob \| history
src/jalview/math/Matrix.java		diff \| blob \| history
src/jalview/math/RotatableMatrix.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/Blosum62ColourScheme.java		diff \| blob \| history
src/jalview/schemes/BuriedColourScheme.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeI.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/Consensus.java		diff \| blob \| history
src/jalview/schemes/HelixColourScheme.java		diff \| blob \| history
src/jalview/schemes/HydrophobicColourScheme.java		diff \| blob \| history
src/jalview/schemes/NucleotideColourScheme.java		diff \| blob \| history
src/jalview/schemes/PIDColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/schemes/ScoreColourScheme.java		diff \| blob \| history
src/jalview/schemes/StrandColourScheme.java		diff \| blob \| history
src/jalview/schemes/TaylorColourScheme.java		diff \| blob \| history
src/jalview/schemes/TurnColourScheme.java		diff \| blob \| history
src/jalview/schemes/UserColourScheme.java		diff \| blob \| history
src/jalview/schemes/ZappoColourScheme.java		diff \| blob \| history
src/jalview/util/BrowserLauncher.java		diff \| blob \| history
src/jalview/util/Comparison.java		diff \| blob \| history
src/jalview/util/DBRefUtils.java		diff \| blob \| history
src/jalview/util/ImageMaker.java		diff \| blob \| history
src/jalview/util/QuickSort.java		diff \| blob \| history
src/jalview/ws/Discoverer.java		diff \| blob \| history
src/jalview/ws/JPredClient.java		diff \| blob \| history
src/jalview/ws/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/WSClient.java		diff \| blob \| history
src/jalview/ws/WSClientI.java		diff \| blob \| history
src/vamsas/IMsaWS.java		diff \| blob \| history
src/vamsas/objects/simple/Alignment.java		diff \| blob \| history
src/vamsas/objects/simple/Alignment_Helper.java		diff \| blob \| history
src/vamsas/objects/simple/MsaResult.java		diff \| blob \| history
src/vamsas/objects/simple/MsaResult_Helper.java		diff \| blob \| history
src/vamsas/objects/simple/Object.java		diff \| blob \| history
src/vamsas/objects/simple/Object_Helper.java		diff \| blob \| history
src/vamsas/objects/simple/SequenceSet.java		diff \| blob \| history
src/vamsas/objects/simple/SequenceSet_Helper.java		diff \| blob \| history
src/vamsas/objects/simple/WsJobId.java		diff \| blob \| history
src/vamsas/objects/simple/WsJobId_Helper.java		diff \| blob \| history

RSS Atom