JAL-1793 spike branch updated to latest
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 27 Oct 2017 09:54:03 +0000 (10:54 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 27 Oct 2017 09:54:03 +0000 (10:54 +0100)
commit14193747f3831242bc7dfac12394eb20eb0ba480
treeff2ebafee5244d7d6e91d17a51ecb1a2e53a5eda
parenta57976ba40e1abe6d7c1940386e1a25419ef9c9d
JAL-1793 spike branch updated to latest
85 files changed:
RELEASE
build.xml
help/html/calculations/pairwise.html
help/html/releases.html
src/MCview/AppletPDBCanvas.java
src/MCview/PDBCanvas.java
src/jalview/analysis/AlignSeq.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AppletJmol.java
src/jalview/appletgui/AppletJmolBinding.java
src/jalview/appletgui/ExtJmol.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/PaintRefresher.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/Mapping.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/features/FeatureAttributeType.java [new file with mode: 0644]
src/jalview/datamodel/features/FeatureSource.java [new file with mode: 0644]
src/jalview/datamodel/features/FeatureSourceI.java [new file with mode: 0644]
src/jalview/datamodel/features/FeatureSources.java [new file with mode: 0644]
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblSymbol.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/AquaInternalFrameManager.java [new file with mode: 0644]
src/jalview/gui/CalculationChooser.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/CrossRefAction.java
src/jalview/gui/CutAndPasteHtmlTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FontChooser.java
src/jalview/gui/IProgressIndicator.java
src/jalview/gui/IdPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PaintRefresher.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/ProgressBar.java
src/jalview/gui/PromptUserConfig.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/StructureViewerBase.java
src/jalview/gui/TreePanel.java
src/jalview/gui/ViewSelectionMenu.java
src/jalview/io/FileLoader.java
src/jalview/io/InputStreamParser.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/vcf/VCFLoader.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/MouseOverStructureListener.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/util/MappingUtils.java
src/jalview/util/StringUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/viewmodel/ViewportRanges.java
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
test/jalview/analysis/AlignmentGenerator.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/TestAlignSeq.java
test/jalview/datamodel/SequenceFeatureTest.java
test/jalview/gui/FreeUpMemoryTest.java [new file with mode: 0644]
test/jalview/gui/PairwiseAlignmentPanelTest.java [new file with mode: 0644]
test/jalview/gui/ProgressBarTest.java
test/jalview/io/vcf/VCFLoaderTest.java
test/jalview/io/vcf/testVcf.dat
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/util/StringUtilsTest.java
test/jalview/viewmodel/ViewportRangesTest.java