Merge branch 'develop' into menard
authorjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 15 Nov 2012 15:15:04 +0000 (15:15 +0000)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 15 Nov 2012 15:15:04 +0000 (15:15 +0000)
commit28787d9646cca5dd77190930f59b7ff32cf995b4
treec01d2100e74839041db0b49974fd714f7d8f7e44
parentcc407171f5746de69ca1d4af653984d778affeb9
parentfc1071bf1a0ffd7ae13006ddaa2f82a63b35abcd
Merge branch 'develop' into menard

Conflicts:
src/MCview/PDBfile.java
src/jalview/analysis/Rna.java
src/jalview/analysis/StructureFrequency.java
src/jalview/appletgui/AlignFrame.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/PopupMenu.java
src/jalview/io/FeaturesFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/workers/StrucConsensusThread.java
39 files changed:
build.xml
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/jalview/analysis/Rna.java
src/jalview/analysis/StructureFrequency.java
src/jalview/appletgui/AlignFrame.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/Annotation.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AppVarnaBinding.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/PopupMenu.java
src/jalview/io/AlignFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BLCFile.java
src/jalview/io/ClustalFile.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/JalviewFileChooser.java
src/jalview/io/MSFfile.java
src/jalview/io/PIRFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.java
src/jalview/io/SimpleBlastFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GDesktop.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/ResidueProperties.java
src/jalview/workers/StrucConsensusThread.java
test/jalview/io/TCoffeeScoreFileTest.java