Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD
authorJim Procter <j.procter@dundee.ac.uk>
Mon, 21 Nov 2022 17:02:08 +0000 (17:02 +0000)
committerJim Procter <j.procter@dundee.ac.uk>
Mon, 21 Nov 2022 17:02:08 +0000 (17:02 +0000)
commit304e64fb34b32659be1bbfd39fb4e15b2f79586e
treefdffcee1d9cb315f0fa4d63cec2a09a5c2cac752
parentcfb79b69d9fa44595560659bd95d1d1cd27677ad
parent61ff8fb4efa315c35149c9d11850d99e3d00c441
Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD
133 files changed:
THIRDPARTYLIBS
build.gradle
doc/building.html
gradle.properties
help/help/help.jhm
help/help/helpTOC.xml
help/help/html/features/preferences.html
help/help/html/releases.html
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Finder.java
src/jalview/api/AlignViewportI.java
src/jalview/api/FeatureSettingsModelI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/js/MouseOverStructureListener.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/ResidueCount.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/fts/service/pdb/PDBFTSRestClient.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AppJmol.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SplashScreen.java
src/jalview/gui/SplitFrame.java
src/jalview/gui/StructureChooser.java
src/jalview/gui/StructureViewer.java
src/jalview/gui/StructureViewerBase.java
src/jalview/gui/TreeCanvas.java
src/jalview/gui/TreePanel.java
src/jalview/gui/UserDefinedColours.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsPreferences.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BackupFiles.java
src/jalview/io/FileFormat.java
src/jalview/io/FileFormats.java
src/jalview/io/FileLoader.java
src/jalview/io/IdentifyFile.java
src/jalview/io/NewickFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/project/Jalview2XML.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/ColourSchemes.java
src/jalview/schemes/FeatureSettingsAdapter.java
src/jalview/schemes/ResidueProperties.java
src/jalview/structure/StructureImportSettings.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/util/ColorUtils.java
src/jalview/util/Comparison.java
src/jalview/util/DBRefUtils.java
src/jalview/util/HttpUtils.java
src/jalview/util/MapList.java
src/jalview/util/MappingUtils.java
src/jalview/util/MessageManager.java
src/jalview/util/Platform.java
src/jalview/util/StringUtils.java
src/jalview/viewmodel/AlignmentViewport.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/dbsources/EmblCdsSource.java
src/jalview/ws/dbsources/EmblFlatfileSource.java
src/jalview/ws/dbsources/EmblSource.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/MsaWSClient.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/jws2/dm/JabaOption.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/sifts/SiftsClient.java
src/jalview/xml/binding/jalview/DoubleVector.java
src/jalview/xml/binding/jalview/JalviewModel.java
test/jalview/analysis/AlignmentGenerator.java
test/jalview/analysis/FinderTest.java
test/jalview/datamodel/ResidueCountTest.java
test/jalview/datamodel/SequenceTest.java
test/jalview/ext/ensembl/EnsemblCdnaTest.java
test/jalview/ext/ensembl/EnsemblGeneTest.java
test/jalview/ext/jmol/JmolCommandsTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/fts/service/pdb/PDBFTSPanelTest.java
test/jalview/gui/FreeUpMemoryTest.java
test/jalview/gui/SeqCanvasTest.java
test/jalview/gui/SeqPanelTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/BackupFilesTest.java
test/jalview/io/FileFormatsTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/MapListTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/jws2/ParameterUtilsTest.java