JAL-2629 storage and lifecycle of alignment/group HMM annotations revised
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Wed, 7 Mar 2018 10:35:12 +0000 (10:35 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Wed, 7 Mar 2018 10:35:12 +0000 (10:35 +0000)
commit4389a166735bf1203894abdf3cf7dd57c4856dbc
tree73abac2bf3f79068b4ef649dc103b0da89a9ae1c
parent6368dda9a62fdc2e36b2b260666f093e9668dcad
JAL-2629 storage and lifecycle of alignment/group HMM annotations revised
32 files changed:
src/jalview/analysis/AAFrequency.java
src/jalview/api/AlignCalcWorkerI.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/SequenceCollectionI.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
src/jalview/gui/SeqPanel.java
src/jalview/hmmer/HMMAlign.java [moved from src/jalview/hmmer/HMMAlignThread.java with 88% similarity]
src/jalview/hmmer/HMMBuild.java [moved from src/jalview/hmmer/HMMBuildThread.java with 67% similarity]
src/jalview/hmmer/HMMSearch.java [moved from src/jalview/hmmer/HMMSearchThread.java with 91% similarity]
src/jalview/hmmer/HmmerCommand.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/HMMERAlignmentColourScheme.java
src/jalview/schemes/HMMERColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/InformationThread.java
test/jalview/datamodel/SequenceGroupTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/hmmer/HMMERTest.java
test/jalview/io/JSONFileTest.java