Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 21 Aug 2017 13:06:46 +0000 (14:06 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 21 Aug 2017 13:06:46 +0000 (14:06 +0100)
commitbe762d8d9c71a7aa3121e845c45911c7192b7827
tree6dd4061aa63112ef36f946b6fae0f2d149c01fce
parentd1bb7a31fc091606aedbc255a5766ac79e36fa91
parente327ac5df98f528afeb347ac9a79085ad0d0975b
Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
src/MCview/PDBChain.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Dna.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/SeqPanel.java
src/jalview/commands/EditCommand.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/Finder.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/io/FeaturesFile.java
src/jalview/io/JSONFile.java
src/jalview/io/gff/InterProScanHelper.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/util/RangeComparator.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/ws/jws2/AADisorderClient.java
81 files changed:
src/MCview/PDBChain.java
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/Rna.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/FeatureColourChooser.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/SeqCanvas.java
src/jalview/appletgui/SeqPanel.java
src/jalview/commands/EditCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/BinarySequence.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/SearchResults.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/ext/rbvi/chimera/AtomSpecModel.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AppVarna.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/IdPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/TreePanel.java
src/jalview/io/ClustalFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JSONFile.java
src/jalview/io/JnetAnnotationMaker.java
src/jalview/io/MSFfile.java
src/jalview/io/PfamFile.java
src/jalview/io/PhylipFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/StructureFile.java
src/jalview/io/gff/ExonerateHelper.java
src/jalview/io/gff/Gff3Helper.java
src/jalview/io/gff/GffHelperBase.java
src/jalview/io/gff/InterProScanHelper.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/renderer/seqfeatures/FeatureColourFinder.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemes/ClustalxColourScheme.java
src/jalview/schemes/FeatureColour.java
src/jalview/util/Comparison.java
src/jalview/viewmodel/ViewportRanges.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/rest/params/SeqVector.java