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

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

author	BobHanson <hansonr@stolaf.edu>
	Thu, 9 Apr 2020 18:03:44 +0000 (13:03 -0500)
committer	BobHanson <hansonr@stolaf.edu>
	Thu, 9 Apr 2020 18:03:44 +0000 (13:03 -0500)
commit	b87512d6e28a2a93ea2f08dcfbee320856c5c8de
tree	2f1fe4d01a515857addffe0a568155ef42d15ff8	tree \| snapshot
parent	ab0e5f2223a993371761baf240d815abdfcbb950	commit \| diff

temp push

129 files changed:

src/jalview/api/AlignFrameI.java	[new file with mode: 0644]	blob
src/jalview/api/JalviewApp.java	[new file with mode: 0644]	blob
src/jalview/appletgui/AlignFrame.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/EmbmenuFrame.java		diff \| blob \| history
src/jalview/appletgui/FeatureColourChooser.java		diff \| blob \| history
src/jalview/appletgui/FeatureSettings.java		diff \| blob \| history
src/jalview/appletgui/FontChooser.java		diff \| blob \| history
src/jalview/appletgui/IdPanel.java		diff \| blob \| history
src/jalview/appletgui/OverviewCanvas.java		diff \| blob \| history
src/jalview/appletgui/OverviewPanel.java		diff \| blob \| history
src/jalview/appletgui/ScalePanel.java		diff \| blob \| history
src/jalview/appletgui/SeqCanvas.java		diff \| blob \| history
src/jalview/appletgui/TreePanel.java		diff \| blob \| history
src/jalview/bin/AlignViewController.java	[new file with mode: 0644]	blob
src/jalview/bin/AppletParams.java	[new file with mode: 0644]	blob
src/jalview/bin/ArgsParser.java		diff \| blob \| history
src/jalview/bin/AssociatePdbFileWithSeq.java	[new file with mode: 0644]	blob
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewAppLoader.java	[new file with mode: 0644]	blob
src/jalview/bin/JalviewJSApi.java	[new file with mode: 0644]	blob
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/datamodel/features/FeatureStore.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeatures.java		diff \| blob \| history
src/jalview/datamodel/features/SequenceFeaturesI.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblCds.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblGene.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblSeqProxy.java		diff \| blob \| history
src/jalview/gui/APQHandlers.java		diff \| blob \| history
src/jalview/gui/AlignExportOptions.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AnnotationColourChooser.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/AssociatePdbFileWithSeq.java		diff \| blob \| history
src/jalview/gui/CalculationChooser.java		diff \| blob \| history
src/jalview/gui/ChimeraViewFrame.java		diff \| blob \| history
src/jalview/gui/ColourMenuHelper.java		diff \| blob \| history
src/jalview/gui/CrossRefAction.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FeatureEditor.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/IdPanel.java		diff \| blob \| history
src/jalview/gui/JalviewDialog.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/LineartOptions.java		diff \| blob \| history
src/jalview/gui/OOMWarning.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/PromptUserConfig.java		diff \| blob \| history
src/jalview/gui/SeqPanel.java		diff \| blob \| history
src/jalview/gui/SequenceFetcher.java		diff \| blob \| history
src/jalview/gui/SplashScreen.java		diff \| blob \| history
src/jalview/gui/SplitFrame.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/StructureViewer.java		diff \| blob \| history
src/jalview/gui/StructureViewerBase.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/gui/UserQuestionnaireCheck.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/FeaturesFile.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/WSWUBlastClient.java		diff \| blob \| history
src/jalview/io/gff/Gff3Helper.java		diff \| blob \| history
src/jalview/io/gff/InterProScanHelper.java		diff \| blob \| history
src/jalview/io/gff/SequenceOntologyFactory.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencemapping.java		diff \| blob \| history
src/jalview/javascript/JSFunctionExec.java		diff \| blob \| history
src/jalview/javascript/JalviewLiteJsApi.java		diff \| blob \| history
src/jalview/javascript/MouseOverListener.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GSequenceLink.java		diff \| blob \| history
src/jalview/project/Jalview2XML.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/util/Platform.java		diff \| blob \| history
src/jalview/util/ShortcutKeyMaskExWrapper.java		diff \| blob \| history
src/jalview/util/StringUtils.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java		diff \| blob \| history
src/jalview/ws/DBRefFetcher.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/SequenceFetcherFactory.java		diff \| blob \| history
src/jalview/ws/jws1/Discoverer.java		diff \| blob \| history
src/jalview/ws/jws1/JPredClient.java		diff \| blob \| history
src/jalview/ws/jws1/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws1/SeqSearchWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Client.java		diff \| blob \| history
src/jalview/ws/jws2/Jws2Discoverer.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/SequenceAnnotationWSClient.java		diff \| blob \| history
src/jalview/ws/jws2/jabaws2/Jws2Instance.java		diff \| blob \| history
src/jalview/ws/rest/RestClient.java		diff \| blob \| history
src/jalview/ws/seqfetcher/ASequenceFetcher.java		diff \| blob \| history
src/jalview/ws/seqfetcher/DbSourceProxyRoot.java	[new file with mode: 0644]	blob
test/jalview/analysis/FinderTest.java		diff \| blob \| history
test/jalview/ext/jmol/JmolParserTest.java		diff \| blob \| history
test/jalview/ext/jmol/JmolViewerTest.java		diff \| blob \| history
test/jalview/ext/rbvi/chimera/FeatureRenderer.java	[new file with mode: 0644]	blob
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java		diff \| blob \| history
test/jalview/gui/AlignFrameTest.java		diff \| blob \| history
test/jalview/gui/AlignViewportTest.java		diff \| blob \| history
test/jalview/gui/AlignmentPanelTest.java		diff \| blob \| history
test/jalview/gui/AnnotationChooserTest.java		diff \| blob \| history
test/jalview/gui/AnnotationColumnChooserTest.java		diff \| blob \| history
test/jalview/gui/AnnotationRowFilterTest.java		diff \| blob \| history
test/jalview/gui/CalculationChooserTest.java		diff \| blob \| history
test/jalview/gui/FreeUpMemoryTest.java		diff \| blob \| history
test/jalview/gui/SeqPanelTest.java		diff \| blob \| history
test/jalview/io/AnnotatedPDBFileInputTest.java		diff \| blob \| history
test/jalview/io/CrossRef2xmlTests.java		diff \| blob \| history
test/jalview/io/Jalview2xmlBase.java		diff \| blob \| history
test/jalview/io/JalviewExportPropertiesTests.java		diff \| blob \| history
test/jalview/project/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/schemes/ColourSchemesTest.java		diff \| blob \| history
test/jalview/structure/StructureSelectionManagerTest.java		diff \| blob \| history
test/jalview/ws/PDBSequenceFetcherTest.java		diff \| blob \| history
test/jalview/ws/dbsources/RemoteFormatTest.java		diff \| blob \| history
test/mc_view/PDBfileTest.java		diff \| blob \| history

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