Merge branch 'develop' into features/filetypeEnum
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 30 Aug 2016 11:56:34 +0000 (12:56 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 30 Aug 2016 11:56:34 +0000 (12:56 +0100)
commit8b27085fa7fc5f2877e078421284c2636b85b8c6
tree049eb548306a6a6d9b0164c561d8ef0d40dd3cab
parent4a5137b64f7ec23db2a09290bfcd392984a52150
parentddd696878955d609d942c4173dd66a0da9572741
Merge branch 'develop' into features/filetypeEnum

Conflicts:
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FormatAdapter.java
src/jalview/io/MSFfile.java
src/jalview/io/RnamlFile.java
src/jalview/io/StockholmFile.java
src/jalview/ws/dbsources/Pdb.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/ws/jabaws/RNAStructExportImport.java
60 files changed:
src/MCview/PDBfile.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.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/JmolParser.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.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/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/WsParamSetManager.java
src/jalview/io/AlignFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/FileFormat.java
src/jalview/io/HTMLOutput.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/JSONFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/MSFfile.java
src/jalview/io/PfamFile.java
src/jalview/io/RnamlFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/StructureFile.java
src/jalview/jbgui/GFinder.java
src/jalview/structure/StructureImportSettings.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/util/ImageMaker.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/jws1/Annotate3D.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/rest/params/Alignment.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/DnaTest.java
test/jalview/datamodel/AlignmentAnnotationTests.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/AnnotatedPDBFileInputTest.java
test/jalview/io/FormatAdapterTest.java
test/jalview/io/Jalview2xmlTests.java
test/jalview/io/StockholmFileTest.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/sifts/SiftsClientTest.java