file format enum wip changes
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 11 Jul 2016 20:30:45 +0000 (21:30 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Mon, 11 Jul 2016 20:30:45 +0000 (21:30 +0100)
commitee198b3ca3687f18a2ee186f4e7c7330f4ea30f0
tree39b96aebc1ec0985bbbe115445e32161f1055f70
parent0bec4854366c4bc4608ed0d7dc1506fc6afe2285
file format enum wip changes
102 files changed:
src/MCview/AppletPDBCanvas.java
src/MCview/AppletPDBViewer.java
src/MCview/PDBCanvas.java
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/jalview/api/AlignViewControllerI.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/datamodel/PDBEntry.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolParser.java
src/jalview/gui/AlignExportSettings.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationChooser.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Preferences.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/StructureViewerBase.java
src/jalview/io/AlignFile.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BLCFile.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/ClustalFile.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/FormatAdapter.java
src/jalview/io/HtmlFile.java
src/jalview/io/HtmlSvgOutput.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JSONFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/MSFfile.java
src/jalview/io/NewickFile.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PhylipFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/RnamlFile.java
src/jalview/io/SimpleBlastFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/StructureFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/jbgui/GAlignExportSettings.java
src/jalview/jbgui/GDesktop.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/structures/models/AAStructureBindingModel.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/SeqSearchWSThread.java
test/MCview/PDBfileTest.java
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/DnaTest.java
test/jalview/analysis/scoremodels/FeatureScoreModelTest.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/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/FeaturesFileTest.java
test/jalview/io/FileIOTester.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