Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
authorJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Mar 2015 15:40:33 +0000 (15:40 +0000)
committerJim Procter <jprocter@dundee.ac.uk>
Fri, 6 Mar 2015 15:40:33 +0000 (15:40 +0000)
commite309b8d9bd62fb304fdd612c7385e76027d2f2d7
tree89f66b9cc1c4fb338ace79c3bdba6a33bfa735a5
parent286715d8408510556366a454a748daf8f60444f1
parentad15cff29620f960119f80176f1fd443da9f6763
Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
JAL-1645 bring JAL-845 feature branch up to date ready for develop merge

Conflicts:
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
test/jalview/analysis/DnaTranslation.java
126 files changed:
help/html/features/multipleViews.html
schemas/jalview.xsd
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
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/TreeCanvas.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/commands/ChangeCaseCommand.java
src/jalview/commands/EditCommand.java
src/jalview/commands/OrderCommand.java
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/ColumnSelection.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/Sequence.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/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/Desktop.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/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/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/FileLoader.java
src/jalview/io/MSFfile.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/GPreferences.java
src/jalview/jbgui/GTreePanel.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/AwtRenderPanelI.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/SequenceListener.java
src/jalview/structure/StructureListener.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structure/VamsasListener.java
src/jalview/util/Comparison.java
src/jalview/util/MapList.java
src/jalview/util/QuickSort.java
src/jalview/util/ShiftList.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/AWSThread.java
src/jalview/ws/jws2/JPred301Client.java
src/jalview/ws/jws2/MsaWSThread.java
src/jalview/ws/rest/RestServiceDescription.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/io/Jalview2xmlTests.java