Merge develop to Release_2_8_3_Branch
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 26 Mar 2015 11:14:54 +0000 (11:14 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 26 Mar 2015 11:14:54 +0000 (11:14 +0000)
commitbe32c14cd8e48fe0a207cd7030cb9cd46f894678
treecd9e59ec92ef338fbdd39e81e018e045257d5b93
parent10e637daad8983c41db8679baabea5563d7371f4
Merge develop to Release_2_8_3_Branch
250 files changed:
.classpath
examples-jbake/templates/jvl_examples.ftl
examples/applets.html
examples/estrogenReceptorCdna.fa [new file with mode: 0644]
examples/estrogenReceptorProtein.fa [new file with mode: 0644]
help/html/features/multipleViews.html
lib/jersey-client-1.19.jar [new file with mode: 0644]
lib/jersey-core-1.19.jar [new file with mode: 0644]
lib/jersey-json-1.19.jar [new file with mode: 0644]
lib/jsr311-api-1.1.1.jar [new file with mode: 0644]
resources/images/dna.png [new file with mode: 0644]
resources/images/error.png [new file with mode: 0644]
resources/images/good.png [new file with mode: 0644]
resources/images/loading.gif [new file with mode: 0644]
resources/images/protein.png [new file with mode: 0644]
resources/images/sugar.png [new file with mode: 0644]
resources/lang/Messages.properties
schemas/jalview.xsd
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
src/ext/vamsas/ServiceHandle.java
src/ext/vamsas/ServiceHandles.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CodingUtils.java [new file with mode: 0644]
src/jalview/analysis/CodonComparator.java [new file with mode: 0644]
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/SequenceIdMatcher.java
src/jalview/analysis/StructureFrequency.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
src/jalview/api/SplitContainerI.java [new file with mode: 0644]
src/jalview/api/ViewStyleI.java [new file with mode: 0644]
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdCanvas.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SequenceRenderer.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/SplitFrame.java [new file with mode: 0644]
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/JalviewLite.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/EditCommand.java
src/jalview/commands/OrderCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignedCodon.java [new file with mode: 0644]
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentOrder.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/ColumnSelection.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/DBRefSource.java
src/jalview/datamodel/IncompleteCodonException.java [new file with mode: 0644]
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AppVarnaBinding.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/DasSourceBrowser.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/IdwidthAdjuster.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PDBSearchPanel.java [new file with mode: 0644]
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/RotatableCanvas.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SequenceRenderer.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SplitFrame.java [new file with mode: 0644]
src/jalview/gui/StructureChooser.java [new file with mode: 0644]
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WsJobParameters.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/FileLoader.java
src/jalview/io/MSFfile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/vamsas/Rangetype.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/io/vamsas/Tree.java
src/jalview/javascript/MouseOverListener.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPDBSearchPanel.java [new file with mode: 0644]
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GSplitFrame.java [new file with mode: 0644]
src/jalview/jbgui/GStructureChooser.java [new file with mode: 0644]
src/jalview/jbgui/GTreePanel.java
src/jalview/jbgui/PDBDocFieldPreferences.java [new file with mode: 0644]
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AwtRenderPanelI.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemabinding/version2/Viewport.java
src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/structure/AtomSpec.java [new file with mode: 0644]
src/jalview/structure/CommandListener.java [new file with mode: 0644]
src/jalview/structure/SequenceListener.java
src/jalview/structure/StructureListener.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structure/VamsasListener.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/Format.java
src/jalview/util/MapList.java
src/jalview/util/MappingUtils.java [new file with mode: 0644]
src/jalview/util/MessageManager.java
src/jalview/util/ParseHtmlBodyAndLinks.java
src/jalview/util/QuickSort.java
src/jalview/util/ReverseListIterator.java [new file with mode: 0644]
src/jalview/util/ShiftList.java
src/jalview/util/StringUtils.java [new file with mode: 0644]
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/viewmodel/styles/ViewStyle.java [new file with mode: 0644]
src/jalview/workers/AlignCalcManager.java
src/jalview/workers/ComplementConsensusThread.java [new file with mode: 0644]
src/jalview/workers/ConsensusThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/AWSThread.java
src/jalview/ws/HttpClientUtils.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/dbsources/PDBRestClient.java [new file with mode: 0644]
src/jalview/ws/jws2/JPred301Client.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/uimodel/PDBRestRequest.java [new file with mode: 0644]
src/jalview/ws/uimodel/PDBRestResponse.java [new file with mode: 0644]
src/uk/ac/ebi/picr/model/CrossReference.java
src/uk/ac/ebi/picr/model/UPEntry.java
src/uk/ac/ebi/www/Data.java
src/uk/ac/ebi/www/InputParams.java
src/uk/ac/ebi/www/WSFile.java
src/vamsas/objects/simple/Alignment.java
src/vamsas/objects/simple/JpredResult.java
src/vamsas/objects/simple/MsaResult.java
src/vamsas/objects/simple/Msfalignment.java
src/vamsas/objects/simple/Object.java
src/vamsas/objects/simple/Result.java
src/vamsas/objects/simple/Secstructpred.java
src/vamsas/objects/simple/SeqSearchResult.java
src/vamsas/objects/simple/Sequence.java
src/vamsas/objects/simple/SequenceSet.java
src/vamsas/objects/simple/WsJobId.java
test/jalview/analysis/AAFrequencyTest.java [new file with mode: 0644]
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/CodingUtilsTest.java [new file with mode: 0644]
test/jalview/analysis/CrossRefTest.java [new file with mode: 0644]
test/jalview/analysis/DnaAlignmentGenerator.java [new file with mode: 0644]
test/jalview/analysis/DnaTest.java [new file with mode: 0644]
test/jalview/analysis/DnaTranslation.java [deleted file]
test/jalview/analysis/TestAlignSeq.java
test/jalview/commands/EditCommandTest.java
test/jalview/datamodel/AlignedCodonFrameTest.java [new file with mode: 0644]
test/jalview/datamodel/AlignedCodonIteratorTest.java [new file with mode: 0644]
test/jalview/datamodel/AlignedCodonTest.java [new file with mode: 0644]
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/ColumnSelectionTest.java [new file with mode: 0644]
test/jalview/datamodel/DBRefEntryTest.java [new file with mode: 0644]
test/jalview/datamodel/SearchResultsTest.java [new file with mode: 0644]
test/jalview/datamodel/SequenceTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/ext/rbvi/chimera/ChimeraConnect.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/JvSwingUtilsTest.java [new file with mode: 0644]
test/jalview/gui/PDBSearchPanelTest.java [new file with mode: 0644]
test/jalview/gui/PaintRefresherTest.java [new file with mode: 0644]
test/jalview/gui/PopupMenuTest.java
test/jalview/gui/StructureChooserTest.java [new file with mode: 0644]
test/jalview/io/AnnotatedPDBFileInputTest.java
test/jalview/io/HtmlFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/pdb_request_json_error.txt [new file with mode: 0644]
test/jalview/io/pdb_response_json.txt [new file with mode: 0644]
test/jalview/schemes/DnaCodonTests.java
test/jalview/schemes/ResiduePropertiesTest.java [new file with mode: 0644]
test/jalview/structure/Mapping.java
test/jalview/structure/StructureSelectionManagerTest.java [new file with mode: 0644]
test/jalview/util/ComparisonTest.java [new file with mode: 0644]
test/jalview/util/MapListTest.java [new file with mode: 0644]
test/jalview/util/MappingUtilsTest.java [new file with mode: 0644]
test/jalview/util/QuickSortTest.java [new file with mode: 0644]
test/jalview/util/ShiftListTest.java [new file with mode: 0644]
test/jalview/util/StringUtilsTest.java [new file with mode: 0644]
test/jalview/viewmodel/styles/TestviewStyle.java [new file with mode: 0644]
test/jalview/ws/dbsources/PDBRestClientTest.java [new file with mode: 0644]
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/rest/ShmmrRSBSService.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java