Merge branch 'develop' into trialMerge
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 28 Nov 2016 17:31:30 +0000 (17:31 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 28 Nov 2016 17:31:30 +0000 (17:31 +0000)
commit483e7163b1fb8d4bcb9393014816c944befce328
tree43798a7a39a967ab5ad203e11af26a079fb6db47
parent70f62620b5f6158be5cd42560d549b2ea4e20c52
parent19424d4e1623bfcdcf30567f7a233fe81c4a9e4e
Merge branch 'develop' into trialMerge

Conflicts:
src/jalview/gui/CutAndPasteTransfer.java
test/MCview/PDBfileTest.java
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/FinderTest.java
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
test/jalview/controller/AlignViewControllerTest.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/io/gff/ExonerateHelperTest.java
test/jalview/io/gff/GffTests.java
test/jalview/structure/Mapping.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/sifts/SiftsClientTest.java
67 files changed:
src/MCview/PDBViewer.java
src/jalview/gui/AlignExportSettings.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/StructureViewerBase.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/WsParamSetManager.java
src/jalview/io/FileLoader.java
src/jalview/io/JalviewFileChooser.java
src/jalview/jbgui/GAlignFrame.java
test/MCview/PDBfileTest.java
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/DnaAlignmentGenerator.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/FinderTest.java
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
test/jalview/controller/AlignViewControllerTest.java
test/jalview/datamodel/AlignmentAnnotationTests.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/jmol/JmolViewerTest.java
test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
test/jalview/ext/paradise/TestAnnotate3D.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/PopupMenuTest.java
test/jalview/io/AnnotatedPDBFileInputTest.java
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/CrossRef2xmlTests.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/FileIOTester.java
test/jalview/io/FormatAdapterTest.java
test/jalview/io/IdentifyFileTest.java
test/jalview/io/JSONFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/JalviewExportPropertiesTests.java
test/jalview/io/NewickFileTests.java
test/jalview/io/PfamFormatInputTest.java
test/jalview/io/PhylipFileTests.java
test/jalview/io/RNAMLfileTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/io/TCoffeeScoreFileTest.java
test/jalview/io/gff/ExonerateHelperTest.java
test/jalview/io/gff/GffTests.java
test/jalview/structure/Mapping.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/rest/ShmmrRSBSService.java
test/jalview/ws/sifts/SiftsClientTest.java