Merge branch 'develop' into developtomchmmer
authorJim Procter <jprocter@issues.jalview.org>
Tue, 4 Jun 2019 17:22:21 +0000 (18:22 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Tue, 4 Jun 2019 17:22:21 +0000 (18:22 +0100)
commitb5667f39acdf309cd92881b73edfda591e0acaf4
tree8603af30a7cf008946a3a7694c7eb85cfdb3c8d0
parent1903e771d3dae79e9a57fcc1147efd37e8a51421
parent9e31a59b947882325ffe614bd71fb732d7952a23
Merge branch 'develop' into developtomchmmer
JAL-3285 merged 2.11 develop into the features/mchmmer branch
- need to fix code for migration from Castor to JAXB
- need to check Stockholm file IO and tests
Good luck !
58 files changed:
help/help/help.jhm
help/help/helpTOC.xml
help/help/html/features/preferences.html
help/help/html/menus/alwhmmer.html
resources/lang/Messages.properties
resources/lang/Messages_es.properties
schemas/jalview.xsd
src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/AlignmentI.java
src/jalview/datamodel/AlignmentView.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceCollectionI.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/CalculationChooser.java
src/jalview/gui/Desktop.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/WsParamSetManager.java
src/jalview/io/FileFormat.java
src/jalview/io/FileLoader.java
src/jalview/io/StockholmFile.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/JalviewColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/util/Platform.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/ConsensusThread.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/SequenceGroupTest.java
test/jalview/gui/AlignFrameTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
utils/i18nAnt.xml