Merge branch 'JAL-1445' into develop
authorJim Procter <jprocter@compbio.dundee.ac.uk>
Tue, 18 Feb 2014 17:12:38 +0000 (17:12 +0000)
committerJim Procter <jprocter@compbio.dundee.ac.uk>
Tue, 18 Feb 2014 17:12:38 +0000 (17:12 +0000)
commit8d2724b83aca38ef75d68787cc5939d950467e63
tree628fff8acdf049b99e3182e2c8f979d94fb5a22c
parent80c223c45fde0899c9794e887801dd82fffd3452
parenta5eefc708b5f7aaedcd1640f944dd5b2851ea614
Merge branch 'JAL-1445' into develop
Carried over source formatting from 2.8.0b1 release

Conflicts:
src/jalview/analysis/StructureFrequency.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AppVarna.java
src/jalview/gui/PopupMenu.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GDesktop.java
38 files changed:
THIRDPARTYLIBS
build.xml
src/MCview/PDBViewer.java
src/MCview/PDBfile.java
src/jalview/analysis/AlignSeq.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/Desktop.java
src/jalview/gui/PopupMenu.java
src/jalview/io/AlignFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FastaFile.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/IdentifyFile.java
src/jalview/io/JPredFile.java
src/jalview/io/PfamFile.java
src/jalview/io/PileUpfile.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/util/DBRefUtils.java
src/jalview/ws/dbsources/Pdb.java
test/jalview/io/TCoffeeScoreFileTest.java