JAL-3210 Merge branch 'develop' into trialMerge
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 16 Jul 2019 07:14:32 +0000 (08:14 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Tue, 16 Jul 2019 07:14:32 +0000 (08:14 +0100)
commit17e4ea278bc9a5fb280db1252ce78b7a295215f5
tree379ce4ae06d4aeaa3c8b9e2ec46af43bc42e6a6c
parente6267883ffc25d76313c9e45967efe2c9e6d1d08
parentfa2429b3c8cd5eb56c4a56572af6e9c4adc916c9
JAL-3210 Merge branch 'develop' into trialMerge

Conflicts:
.classpath
.project
.settings/org.eclipse.jdt.core.prefs
.settings/org.eclipse.jdt.ui.prefs
build.xml
resources/lang/Messages_es.properties
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/jalview/analysis/AAFrequency.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/ensembl/EnsemblMap.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/fts/service/pdb/PDBFTSRestClient.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureTypeSettings.java
src/jalview/gui/WebserviceInfo.java
src/jalview/io/BackupFiles.java
src/jalview/io/FileLoader.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/util/ImageMaker.java
src/jalview/util/Platform.java
src/jalview/ws/SequenceFetcher.java
76 files changed:
.classpath
.project
.settings/org.eclipse.jdt.core.prefs
.settings/org.eclipse.jdt.ui.prefs
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Conservation.java
src/jalview/analysis/StructureFrequency.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/commands/EditCommand.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/DBRefEntry.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/ensembl/EnsemblFeatures.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblMap.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/fts/core/FTSRestClient.java
src/jalview/fts/service/pdb/PDBFTSRestClient.java
src/jalview/gui/APQHandlers.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AppJmol.java
src/jalview/gui/BlogReader.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/CrossRefAction.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FeatureTypeSettings.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/Preferences.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/WebserviceInfo.java
src/jalview/io/AnnotationFile.java
src/jalview/io/BackupFiles.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/JPredFile.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/vamsas/Tree.java
src/jalview/io/vcf/VCFLoader.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/util/ImageMaker.java
src/jalview/util/Platform.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/ws/DBRefFetcher.java
src/jalview/ws/SequenceFetcher.java
src/org/jibble/epsgraphics/EpsGraphics2D.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/io/vcf/VCFLoaderTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/ws/SequenceFetcherTest.java