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

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

author	gmungoc <g.m.carstairs@dundee.ac.uk>
	Thu, 26 Mar 2015 11:14:54 +0000 (11:14 +0000)
committer	gmungoc <g.m.carstairs@dundee.ac.uk>
	Thu, 26 Mar 2015 11:14:54 +0000 (11:14 +0000)
commit	be32c14cd8e48fe0a207cd7030cb9cd46f894678
tree	cd9e59ec92ef338fbdd39e81e018e045257d5b93	tree \| snapshot
parent	10e637daad8983c41db8679baabea5563d7371f4	commit \| diff

Merge develop to Release_2_8_3_Branch

250 files changed:

.classpath		diff \| blob \| history
examples-jbake/templates/jvl_examples.ftl		diff \| blob \| history
examples/applets.html		diff \| blob \| history
examples/estrogenReceptorCdna.fa	[new file with mode: 0644]	blob
examples/estrogenReceptorProtein.fa	[new file with mode: 0644]	blob
help/html/features/multipleViews.html		diff \| blob \| history
lib/jersey-client-1.19.jar	[new file with mode: 0644]	blob
lib/jersey-core-1.19.jar	[new file with mode: 0644]	blob
lib/jersey-json-1.19.jar	[new file with mode: 0644]	blob
lib/jsr311-api-1.1.1.jar	[new file with mode: 0644]	blob
resources/images/dna.png	[new file with mode: 0644]	blob
resources/images/error.png	[new file with mode: 0644]	blob
resources/images/good.png	[new file with mode: 0644]	blob
resources/images/loading.gif	[new file with mode: 0644]	blob
resources/images/protein.png	[new file with mode: 0644]	blob
resources/images/sugar.png	[new file with mode: 0644]	blob
resources/lang/Messages.properties		diff \| blob \| history
schemas/jalview.xsd		diff \| blob \| history
src/MCview/AppletPDBCanvas.java		diff \| blob \| history
src/MCview/Atom.java		diff \| blob \| history
src/MCview/PDBCanvas.java		diff \| blob \| history
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java		diff \| blob \| history
src/ext/vamsas/ServiceHandle.java		diff \| blob \| history
src/ext/vamsas/ServiceHandles.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/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/CodingUtils.java	[new file with mode: 0644]	blob
src/jalview/analysis/CodonComparator.java	[new file with mode: 0644]	blob
src/jalview/analysis/CrossRef.java		diff \| blob \| history
src/jalview/analysis/Dna.java		diff \| blob \| history
src/jalview/analysis/SequenceIdMatcher.java		diff \| blob \| history
src/jalview/analysis/StructureFrequency.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/AlignmentViewPanel.java		diff \| blob \| history
src/jalview/api/SplitContainerI.java	[new file with mode: 0644]	blob
src/jalview/api/ViewStyleI.java	[new file with mode: 0644]	blob
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/AnnotationLabels.java		diff \| blob \| history
src/jalview/appletgui/AnnotationPanel.java		diff \| blob \| history
src/jalview/appletgui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/appletgui/EmbmenuFrame.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/RedundancyPanel.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/SplitFrame.java	[new file with mode: 0644]	blob
src/jalview/appletgui/TreeCanvas.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/commands/ChangeCaseCommand.java		diff \| blob \| history
src/jalview/commands/EditCommand.java		diff \| blob \| history
src/jalview/commands/OrderCommand.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/datamodel/AlignedCodon.java	[new file with mode: 0644]	blob
src/jalview/datamodel/AlignedCodonFrame.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/AlignmentView.java		diff \| blob \| history
src/jalview/datamodel/ColumnSelection.java		diff \| blob \| history
src/jalview/datamodel/DBRefEntry.java		diff \| blob \| history
src/jalview/datamodel/DBRefSource.java		diff \| blob \| history
src/jalview/datamodel/IncompleteCodonException.java	[new file with mode: 0644]	blob
src/jalview/datamodel/Mapping.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/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/ext/jmol/JalviewJmolBinding.java		diff \| blob \| history
src/jalview/ext/paradise/Annotate3D.java		diff \| blob \| history
src/jalview/ext/rbvi/chimera/ChimeraCommands.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/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AlignmentPanel.java		diff \| blob \| history
src/jalview/gui/AnnotationExporter.java		diff \| blob \| history
src/jalview/gui/AnnotationLabels.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/CutAndPasteHtmlTransfer.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/DasSourceBrowser.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/Jalview2XML_V1.java		diff \| blob \| history
src/jalview/gui/JvSwingUtils.java		diff \| blob \| history
src/jalview/gui/OverviewPanel.java		diff \| blob \| history
src/jalview/gui/PCAPanel.java		diff \| blob \| history
src/jalview/gui/PDBSearchPanel.java	[new file with mode: 0644]	blob
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/SplitFrame.java	[new file with mode: 0644]	blob
src/jalview/gui/StructureChooser.java	[new file with mode: 0644]	blob
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/WsJobParameters.java		diff \| blob \| history
src/jalview/io/AppletFormatAdapter.java		diff \| blob \| history
src/jalview/io/BioJsHTMLOutput.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/MSFfile.java		diff \| blob \| history
src/jalview/io/SequenceAnnotationReport.java		diff \| blob \| history
src/jalview/io/StockholmFile.java		diff \| blob \| history
src/jalview/io/VamsasAppDatastore.java		diff \| blob \| history
src/jalview/io/vamsas/Rangetype.java		diff \| blob \| history
src/jalview/io/vamsas/Sequencemapping.java		diff \| blob \| history
src/jalview/io/vamsas/Tree.java		diff \| blob \| history
src/jalview/javascript/MouseOverListener.java		diff \| blob \| history
src/jalview/javascript/MouseOverStructureListener.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GPDBSearchPanel.java	[new file with mode: 0644]	blob
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/jbgui/GSplitFrame.java	[new file with mode: 0644]	blob
src/jalview/jbgui/GStructureChooser.java	[new file with mode: 0644]	blob
src/jalview/jbgui/GTreePanel.java		diff \| blob \| history
src/jalview/jbgui/PDBDocFieldPreferences.java	[new file with mode: 0644]	blob
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/AwtRenderPanelI.java		diff \| blob \| history
src/jalview/renderer/seqfeatures/FeatureRenderer.java		diff \| blob \| history
src/jalview/schemabinding/version2/Viewport.java		diff \| blob \| history
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/structure/AtomSpec.java	[new file with mode: 0644]	blob
src/jalview/structure/CommandListener.java	[new file with mode: 0644]	blob
src/jalview/structure/SequenceListener.java		diff \| blob \| history
src/jalview/structure/StructureListener.java		diff \| blob \| history
src/jalview/structure/StructureSelectionManager.java		diff \| blob \| history
src/jalview/structure/VamsasListener.java		diff \| blob \| history
src/jalview/structures/models/AAStructureBindingModel.java		diff \| blob \| history
src/jalview/util/Comparison.java		diff \| blob \| history
src/jalview/util/DBRefUtils.java		diff \| blob \| history
src/jalview/util/Format.java		diff \| blob \| history
src/jalview/util/MapList.java		diff \| blob \| history
src/jalview/util/MappingUtils.java	[new file with mode: 0644]	blob
src/jalview/util/MessageManager.java		diff \| blob \| history
src/jalview/util/ParseHtmlBodyAndLinks.java		diff \| blob \| history
src/jalview/util/QuickSort.java		diff \| blob \| history
src/jalview/util/ReverseListIterator.java	[new file with mode: 0644]	blob
src/jalview/util/ShiftList.java		diff \| blob \| history
src/jalview/util/StringUtils.java	[new file with mode: 0644]	blob
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java		diff \| blob \| history
src/jalview/viewmodel/styles/ViewStyle.java	[new file with mode: 0644]	blob
src/jalview/workers/AlignCalcManager.java		diff \| blob \| history
src/jalview/workers/ComplementConsensusThread.java	[new file with mode: 0644]	blob
src/jalview/workers/ConsensusThread.java		diff \| blob \| history
src/jalview/workers/StrucConsensusThread.java		diff \| blob \| history
src/jalview/ws/AWSThread.java		diff \| blob \| history
src/jalview/ws/HttpClientUtils.java		diff \| blob \| history
src/jalview/ws/SequenceFetcher.java		diff \| blob \| history
src/jalview/ws/dbsources/PDBRestClient.java	[new file with mode: 0644]	blob
src/jalview/ws/jws2/JPred301Client.java		diff \| blob \| history
src/jalview/ws/jws2/MsaWSThread.java		diff \| blob \| history
src/jalview/ws/rest/InputType.java		diff \| blob \| history
src/jalview/ws/uimodel/PDBRestRequest.java	[new file with mode: 0644]	blob
src/jalview/ws/uimodel/PDBRestResponse.java	[new file with mode: 0644]	blob
src/uk/ac/ebi/picr/model/CrossReference.java		diff \| blob \| history
src/uk/ac/ebi/picr/model/UPEntry.java		diff \| blob \| history
src/uk/ac/ebi/www/Data.java		diff \| blob \| history
src/uk/ac/ebi/www/InputParams.java		diff \| blob \| history
src/uk/ac/ebi/www/WSFile.java		diff \| blob \| history
src/vamsas/objects/simple/Alignment.java		diff \| blob \| history
src/vamsas/objects/simple/JpredResult.java		diff \| blob \| history
src/vamsas/objects/simple/MsaResult.java		diff \| blob \| history
src/vamsas/objects/simple/Msfalignment.java		diff \| blob \| history
src/vamsas/objects/simple/Object.java		diff \| blob \| history
src/vamsas/objects/simple/Result.java		diff \| blob \| history
src/vamsas/objects/simple/Secstructpred.java		diff \| blob \| history
src/vamsas/objects/simple/SeqSearchResult.java		diff \| blob \| history
src/vamsas/objects/simple/Sequence.java		diff \| blob \| history
src/vamsas/objects/simple/SequenceSet.java		diff \| blob \| history
src/vamsas/objects/simple/WsJobId.java		diff \| blob \| history
test/jalview/analysis/AAFrequencyTest.java	[new file with mode: 0644]	blob
test/jalview/analysis/AlignmentUtilsTests.java		diff \| blob \| history
test/jalview/analysis/CodingUtilsTest.java	[new file with mode: 0644]	blob
test/jalview/analysis/CrossRefTest.java	[new file with mode: 0644]	blob
test/jalview/analysis/DnaAlignmentGenerator.java	[new file with mode: 0644]	blob
test/jalview/analysis/DnaTest.java	[new file with mode: 0644]	blob
test/jalview/analysis/DnaTranslation.java	[deleted file]	blob \| history
test/jalview/analysis/TestAlignSeq.java		diff \| blob \| history
test/jalview/commands/EditCommandTest.java		diff \| blob \| history
test/jalview/datamodel/AlignedCodonFrameTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/AlignedCodonIteratorTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/AlignedCodonTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/AlignmentTest.java		diff \| blob \| history
test/jalview/datamodel/ColumnSelectionTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/DBRefEntryTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/SearchResultsTest.java	[new file with mode: 0644]	blob
test/jalview/datamodel/SequenceTest.java		diff \| blob \| history
test/jalview/ext/paradise/TestAnnotate3D.java		diff \| blob \| history
test/jalview/ext/rbvi/chimera/ChimeraConnect.java		diff \| blob \| history
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java		diff \| blob \| history
test/jalview/gui/AnnotationChooserTest.java		diff \| blob \| history
test/jalview/gui/JvSwingUtilsTest.java	[new file with mode: 0644]	blob
test/jalview/gui/PDBSearchPanelTest.java	[new file with mode: 0644]	blob
test/jalview/gui/PaintRefresherTest.java	[new file with mode: 0644]	blob
test/jalview/gui/PopupMenuTest.java		diff \| blob \| history
test/jalview/gui/StructureChooserTest.java	[new file with mode: 0644]	blob
test/jalview/io/AnnotatedPDBFileInputTest.java		diff \| blob \| history
test/jalview/io/HtmlFileTest.java		diff \| blob \| history
test/jalview/io/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/io/pdb_request_json_error.txt	[new file with mode: 0644]	blob
test/jalview/io/pdb_response_json.txt	[new file with mode: 0644]	blob
test/jalview/schemes/DnaCodonTests.java		diff \| blob \| history
test/jalview/schemes/ResiduePropertiesTest.java	[new file with mode: 0644]	blob
test/jalview/structure/Mapping.java		diff \| blob \| history
test/jalview/structure/StructureSelectionManagerTest.java	[new file with mode: 0644]	blob
test/jalview/util/ComparisonTest.java	[new file with mode: 0644]	blob
test/jalview/util/MapListTest.java	[new file with mode: 0644]	blob
test/jalview/util/MappingUtilsTest.java	[new file with mode: 0644]	blob
test/jalview/util/QuickSortTest.java	[new file with mode: 0644]	blob
test/jalview/util/ShiftListTest.java	[new file with mode: 0644]	blob
test/jalview/util/StringUtilsTest.java	[new file with mode: 0644]	blob
test/jalview/viewmodel/styles/TestviewStyle.java	[new file with mode: 0644]	blob
test/jalview/ws/dbsources/PDBRestClientTest.java	[new file with mode: 0644]	blob
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java		diff \| blob \| history
test/jalview/ws/jabaws/RNAStructExportImport.java		diff \| blob \| history
test/jalview/ws/rest/ShmmrRSBSService.java		diff \| blob \| history
test/jalview/ws/seqfetcher/DbRefFetcherTest.java		diff \| blob \| history

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