Merge branch 'develop' into trialMerge
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 25 Nov 2016 14:21:34 +0000 (14:21 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 25 Nov 2016 14:21:34 +0000 (14:21 +0000)
commit7d67fb613ec026dc9a265e351e7fab542e3f1d61
tree351b5d7a2234d911ed3ed1d7ccf6cdf13aeea796
parent02e38bb826828ab2991584cf4b737c0138cb6c44
parent3e29fb36af9c48e07837e32b7e99c081b2461b2f
Merge branch 'develop' into trialMerge

Conflicts:
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/ExtJmol.java
src/jalview/datamodel/PDBEntry.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/JalviewChimeraBindingModel.java
src/jalview/gui/StructureChooser.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/HTMLOutput.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/StructureFile.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Xfam.java
test/MCview/PDBfileTest.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/PfamFormatInputTest.java
test/jalview/io/gff/ExonerateHelperTest.java
test/jalview/structure/Mapping.java
test/jalview/structures/models/AAStructureBindingModelTest.java
86 files changed:
src/MCview/AppletPDBCanvas.java
src/MCview/PDBCanvas.java
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/jalview/api/AlignViewControllerI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/ExtJmol.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/PDBEntry.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AppJmolBinding.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/JalviewChimeraBindingModel.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/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileFormat.java
src/jalview/io/HTMLOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JalviewFileView.java
src/jalview/io/MSFfile.java
src/jalview/io/PfamFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/StructureFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/structure/StructureImportSettings.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/util/ImageMaker.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Pfam.java
test/MCview/PDBfileTest.java
test/jalview/analysis/AlignmentUtilsTests.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/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/FormatAdapterTest.java
test/jalview/io/JSONFileTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/NewickFileTests.java
test/jalview/io/PfamFormatInputTest.java
test/jalview/io/StockholmFileTest.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/RNAStructExportImport.java
test/jalview/ws/sifts/SiftsClientTest.java