source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	jprocter <jprocter@compbio.dundee.ac.uk>
	Tue, 22 May 2012 11:20:02 +0000 (12:20 +0100)
committer	jprocter <jprocter@compbio.dundee.ac.uk>
	Tue, 22 May 2012 11:25:34 +0000 (12:25 +0100)
commit	a79f9e113c51c032070c670e45ce3eb464691166
tree	a6012f5df34d8ebe42b9fac9f0141c4d6491ac46	tree \| snapshot
parent	973ea5b735c3725ca2d1208c6dd32f2671069bbb	commit \| diff

Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop
conflicts due to refactoring according to JAL-972, JAL-968, JAL-968
Conflicts:
.classpath
examples/appletParameters.html
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/jbgui/GAlignFrame.java

33 files changed:

.classpath		diff \| blob \| history
.project		diff \| blob \| history
examples/appletParameters.html		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/SequenceRenderer.java		diff \| blob \| history
src/jalview/appletgui/UserDefinedColours.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/datamodel/Alignment.java		diff \| blob \| history
src/jalview/datamodel/AlignmentI.java		diff \| blob \| history
src/jalview/datamodel/AnnotatedCollectionI.java	[new file with mode: 0644]	blob
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/SequenceI.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/SequenceRenderer.java		diff \| blob \| history
src/jalview/gui/UserDefinedColours.java		diff \| blob \| history
src/jalview/io/AlignFile.java		diff \| blob \| history
src/jalview/io/TCoffeeScoreFile.java	[new file with mode: 0644]	blob
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/schemes/AnnotationColourGradient.java		diff \| blob \| history
src/jalview/schemes/Blosum62ColourScheme.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeI.java		diff \| blob \| history
src/jalview/schemes/ColourSchemeProperty.java		diff \| blob \| history
src/jalview/schemes/NucleotideColourScheme.java		diff \| blob \| history
src/jalview/schemes/PIDColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueColourScheme.java		diff \| blob \| history
src/jalview/schemes/ScoreColourScheme.java		diff \| blob \| history
src/jalview/schemes/TCoffeeColourScheme.java	[new file with mode: 0644]	blob
src/jalview/schemes/UserColourScheme.java		diff \| blob \| history
test/jalview/io/TCoffeeScoreFileTest.java	[new file with mode: 0644]	blob
test/jalview/io/tcoffee.fasta_aln	[new file with mode: 0644]	blob
test/jalview/io/tcoffee.score_ascii	[new file with mode: 0644]	blob

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