Merge branch 'develop' into features/hmmer
authorTZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Fri, 18 Aug 2017 16:29:38 +0000 (17:29 +0100)
committerTZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Fri, 18 Aug 2017 16:29:38 +0000 (17:29 +0100)
commitcef7be0f9008ff15318e3479a5de35e127071ef3
treeeae398e8513784ec7399a2219ed097073bd71d34
parent46406ae21c62b964714ce136c9d692985c17211d
parente327ac5df98f528afeb347ac9a79085ad0d0975b
Merge branch 'develop' into features/hmmer

Conflicts:
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/JalviewColourScheme.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/AlignCalcManager.java
35 files changed:
resources/lang/Messages.properties
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentOrder.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/io/AlignFile.java
src/jalview/io/FileFormat.java
src/jalview/io/FileLoader.java
src/jalview/io/HMMFile.java
src/jalview/io/IdentifyFile.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPreferences.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/renderer/ResidueShader.java
src/jalview/renderer/ResidueShaderI.java
src/jalview/schemes/JalviewColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/AlignCalcManager.java
src/jalview/ws/jws2/MsaWSThread.java