JAL-2738 update spike branch with latest
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 24 Oct 2017 12:50:46 +0000 (13:50 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 24 Oct 2017 12:50:46 +0000 (13:50 +0100)
commita57976ba40e1abe6d7c1940386e1a25419ef9c9d
treed0967bafc7294c995e6aeb4deacad0565e46532c
parent353109c11d706b29ae5bc9606f0e12223aa45a98
JAL-2738 update spike branch with latest
90 files changed:
.checkstyle
examples/groovy/PIDmatrix.groovy [new file with mode: 0644]
help/html/releases.html
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java
src/jalview/api/AlignViewportI.java
src/jalview/api/AlignmentViewPanel.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/appletgui/AnnotationColumnChooser.java
src/jalview/appletgui/AnnotationLabels.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/AnnotationRowFilter.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/FeatureSettings.java
src/jalview/appletgui/FontChooser.java
src/jalview/appletgui/IdPanel.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/RedundancyPanel.java
src/jalview/appletgui/ScalePanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/SliderPanel.java
src/jalview/appletgui/SplitFrame.java
src/jalview/appletgui/UserDefinedColours.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/CigarArray.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblGenomes.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblProtein.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/ensembl/EnsemblSymbol.java
src/jalview/ext/ensembl/EnsemblXref.java
src/jalview/ext/ensembl/Species.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/rbvi/chimera/AtomSpecModel.java
src/jalview/fts/service/pdb/PDBFTSPanel.java
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationChooser.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationColumnChooser.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AnnotationRowFilter.java
src/jalview/gui/FeatureColourChooser.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IdPanel.java
src/jalview/gui/IdwidthAdjuster.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/RedundancyPanel.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/StructureViewerBase.java
src/jalview/gui/TextColourChooser.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/io/WSWUBlastClient.java
src/jalview/renderer/ScaleRenderer.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/schemes/RNAHelicesColourChooser.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/workers/AnnotationWorker.java
src/jalview/workers/ColumnCounterSetWorker.java
src/jalview/workers/ConsensusThread.java
src/jalview/workers/ConservationThread.java
src/jalview/workers/StrucConsensusThread.java
src/jalview/ws/DasSequenceFeatureFetcher.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
test/jalview/datamodel/CigarArrayTest.java [new file with mode: 0644]
test/jalview/datamodel/SequenceTest.java
test/jalview/ext/ensembl/EnsemblGeneTest.java
test/jalview/ext/ensembl/EnsemblRestClientTest.java
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
test/jalview/ext/ensembl/SpeciesTest.java [new file with mode: 0644]
test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
test/jalview/gui/AlignmentPanelTest.java
test/jalview/gui/SeqCanvasTest.java [new file with mode: 0644]
test/jalview/renderer/ScaleRendererTest.java
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
utils/checkstyle/checkstyle-suppress.xml
utils/checkstyle/import-control.xml