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

diff --cc help/html/features/multipleViews.html
Simple merge

diff --cc schemas/jalview.xsd
Simple merge

diff --cc src/MCview/AppletPDBCanvas.java
Simple merge

diff --cc src/MCview/Atom.java
Simple merge

diff --cc src/MCview/PDBCanvas.java
Simple merge

diff --cc src/jalview/analysis/AAFrequency.java
Simple merge

diff --cc src/jalview/analysis/AlignSeq.java
Simple merge

diff --cc src/jalview/analysis/AlignmentSorter.java
Simple merge

diff --cc src/jalview/analysis/AlignmentUtils.java
Simple merge

diff --cc src/jalview/analysis/CrossRef.java
Simple merge

diff --cc src/jalview/analysis/Dna.java
Simple merge

diff --cc src/jalview/api/AlignViewportI.java
Simple merge

diff --cc src/jalview/api/AlignmentViewPanel.java
Simple merge

diff --cc src/jalview/appletgui/APopupMenu.java
Simple merge

diff --cc src/jalview/appletgui/AlignFrame.java
Simple merge

diff --cc src/jalview/appletgui/AlignViewport.java
Simple merge

diff --cc src/jalview/appletgui/AlignmentPanel.java
Simple merge

diff --cc src/jalview/appletgui/AnnotationLabels.java
Simple merge

diff --cc src/jalview/appletgui/AnnotationPanel.java
Simple merge

diff --cc src/jalview/appletgui/CutAndPasteTransfer.java
Simple merge

diff --cc src/jalview/appletgui/EmbmenuFrame.java
Simple merge

diff --cc src/jalview/appletgui/FontChooser.java
Simple merge

diff --cc src/jalview/appletgui/IdCanvas.java
Simple merge

diff --cc src/jalview/appletgui/IdPanel.java
Simple merge

diff --cc src/jalview/appletgui/RedundancyPanel.java
Simple merge

diff --cc src/jalview/appletgui/ScalePanel.java
Simple merge

diff --cc src/jalview/appletgui/SeqCanvas.java
Simple merge

diff --cc src/jalview/appletgui/SeqPanel.java
Simple merge

diff --cc src/jalview/appletgui/SequenceRenderer.java
Simple merge

diff --cc src/jalview/appletgui/SliderPanel.java
Simple merge

diff --cc src/jalview/appletgui/TreeCanvas.java
Simple merge

diff --cc src/jalview/appletgui/UserDefinedColours.java
Simple merge

diff --cc src/jalview/bin/Jalview.java
Simple merge

diff --cc src/jalview/bin/JalviewLite.java
Simple merge

diff --cc src/jalview/commands/ChangeCaseCommand.java
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diff --cc src/jalview/commands/EditCommand.java
Simple merge

diff --cc src/jalview/commands/OrderCommand.java
Simple merge

diff --cc src/jalview/datamodel/AlignedCodonFrame.java
Simple merge

diff --cc src/jalview/datamodel/Alignment.java
Simple merge

diff --cc src/jalview/datamodel/AlignmentAnnotation.java
Simple merge

diff --cc src/jalview/datamodel/AlignmentI.java
Simple merge

diff --cc src/jalview/datamodel/AlignmentOrder.java
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diff --cc src/jalview/datamodel/ColumnSelection.java
Simple merge

diff --cc src/jalview/datamodel/Mapping.java
Simple merge

diff --cc src/jalview/datamodel/SearchResults.java
Simple merge

diff --cc src/jalview/datamodel/Sequence.java
Simple merge

diff --cc src/jalview/datamodel/SequenceGroup.java
Simple merge

diff --cc src/jalview/datamodel/SequenceI.java
Simple merge

diff --cc src/jalview/datamodel/xdb/embl/EmblEntry.java
Simple merge

diff --cc src/jalview/ext/jmol/JalviewJmolBinding.java
Simple merge

diff --cc src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
Simple merge

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AlignViewport.java
Simple merge

diff --cc src/jalview/gui/AlignmentPanel.java
Simple merge

diff --cc src/jalview/gui/AnnotationExporter.java
Simple merge

diff --cc src/jalview/gui/AnnotationLabels.java
Simple merge

diff --cc src/jalview/gui/AnnotationPanel.java
Simple merge

diff --cc src/jalview/gui/AppVarnaBinding.java
Simple merge

diff --cc src/jalview/gui/CutAndPasteHtmlTransfer.java
Simple merge

diff --cc src/jalview/gui/CutAndPasteTransfer.java
Simple merge

diff --cc src/jalview/gui/Desktop.java
Simple merge

diff --cc src/jalview/gui/FeatureSettings.java
Simple merge

diff --cc src/jalview/gui/Finder.java
Simple merge

diff --cc src/jalview/gui/FontChooser.java
Simple merge

diff --cc src/jalview/gui/IdCanvas.java
Simple merge

diff --cc src/jalview/gui/IdPanel.java
Simple merge

diff --cc src/jalview/gui/IdwidthAdjuster.java
Simple merge

diff --cc src/jalview/gui/Jalview2XML.java
Simple merge

diff --cc src/jalview/gui/Jalview2XML_V1.java
Simple merge

diff --cc src/jalview/gui/JvSwingUtils.java
Simple merge

diff --cc src/jalview/gui/OverviewPanel.java
Simple merge

diff --cc src/jalview/gui/PCAPanel.java
Simple merge

diff --cc src/jalview/gui/PaintRefresher.java
Simple merge

diff --cc src/jalview/gui/PairwiseAlignPanel.java
Simple merge

diff --cc src/jalview/gui/PopupMenu.java
Simple merge

diff --cc src/jalview/gui/Preferences.java
Simple merge

diff --cc src/jalview/gui/RedundancyPanel.java
Simple merge

diff --cc src/jalview/gui/RotatableCanvas.java
Simple merge

diff --cc src/jalview/gui/ScalePanel.java
Simple merge

diff --cc src/jalview/gui/SeqCanvas.java
Simple merge

diff --cc src/jalview/gui/SeqPanel.java
Simple merge

diff --cc src/jalview/gui/SequenceFetcher.java
Simple merge

diff --cc src/jalview/gui/SequenceRenderer.java
Simple merge

diff --cc src/jalview/gui/SliderPanel.java
Simple merge

diff --cc src/jalview/gui/TextColourChooser.java
Simple merge

diff --cc src/jalview/gui/TreeCanvas.java
Simple merge

diff --cc src/jalview/gui/TreePanel.java
Simple merge

diff --cc src/jalview/gui/UserDefinedColours.java
Simple merge

diff --cc src/jalview/gui/VamsasApplication.java
Simple merge

diff --cc src/jalview/gui/WsJobParameters.java
Simple merge

diff --cc src/jalview/io/AppletFormatAdapter.java
Simple merge

diff --cc src/jalview/io/FileLoader.java
Simple merge

diff --cc src/jalview/io/MSFfile.java
Simple merge

diff --cc src/jalview/io/VamsasAppDatastore.java
Simple merge

diff --cc src/jalview/io/vamsas/Rangetype.java
Simple merge

diff --cc src/jalview/io/vamsas/Sequencemapping.java
Simple merge

diff --cc src/jalview/io/vamsas/Tree.java
Simple merge

diff --cc src/jalview/javascript/MouseOverListener.java
Simple merge

diff --cc src/jalview/javascript/MouseOverStructureListener.java
Simple merge

diff --cc src/jalview/jbgui/GAlignFrame.java
Simple merge

diff --cc src/jalview/jbgui/GPreferences.java
Simple merge

diff --cc src/jalview/jbgui/GTreePanel.java
Simple merge

diff --cc src/jalview/renderer/AnnotationRenderer.java
Simple merge

diff --cc src/jalview/renderer/AwtRenderPanelI.java
Simple merge

diff --cc src/jalview/schemabinding/version2/Viewport.java
Simple merge

diff --cc src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
Simple merge

diff --cc src/jalview/schemes/ClustalxColourScheme.java
Simple merge

diff --cc src/jalview/schemes/ResidueProperties.java
Simple merge

diff --cc src/jalview/structure/SequenceListener.java
Simple merge

diff --cc src/jalview/structure/StructureListener.java
Simple merge

diff --cc src/jalview/structure/StructureSelectionManager.java
Simple merge

diff --cc src/jalview/structure/VamsasListener.java
Simple merge

diff --cc src/jalview/util/Comparison.java
Simple merge

diff --cc src/jalview/util/MapList.java
Simple merge

diff --cc src/jalview/util/QuickSort.java
Simple merge

diff --cc src/jalview/util/ShiftList.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
Simple merge

diff --cc src/jalview/workers/ConsensusThread.java
Simple merge

diff --cc src/jalview/workers/StrucConsensusThread.java
Simple merge

diff --cc src/jalview/ws/AWSThread.java
Simple merge

diff --cc src/jalview/ws/jws2/JPred301Client.java
Simple merge

diff --cc src/jalview/ws/jws2/MsaWSThread.java
Simple merge

diff --cc src/jalview/ws/rest/RestServiceDescription.java
Simple merge

diff --cc test/jalview/analysis/AlignmentUtilsTests.java
Simple merge

diff --cc test/jalview/analysis/TestAlignSeq.java
Simple merge

diff --cc test/jalview/io/Jalview2xmlTests.java
Simple merge