Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
authorJim Procter <j.procter@dundee.ac.uk>
Wed, 14 Dec 2022 16:01:09 +0000 (16:01 +0000)
committerJim Procter <j.procter@dundee.ac.uk>
Wed, 14 Dec 2022 16:01:09 +0000 (16:01 +0000)
commitd043ce47fc710d3eb2629ba926a8a7417bd67d8c
treed1281fd0d196925202fa6779cc3a1aed26e06ec6
parent49db0dff1da16c3355b43a41498c1fc93ef47e91
parent04c8f7bff663aa469127e9eed4164e02933782f1
Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

 Conflicts:
THIRDPARTYLIBS
build.gradle
gradle.properties
help/help/html/features/preferences.html
help/help/html/releases.html
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/datamodel/SequenceI.java
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureEditor.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OverviewPanel.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/UserQuestionnaireCheck.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsParamSetManager.java
src/jalview/io/BackupFiles.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/javascript/log4j/Logger.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/urls/IdentifiersUrlProvider.java
src/jalview/util/HttpUtils.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/AWSThread.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/gui/MsaWSThread.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws2/AADisorderClient.java
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/rest/HttpResultSet.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/utils/UrlDownloadClient.java
src/jalview/xml/binding/jalview/DoubleVector.java
src/jalview/xml/binding/jalview/JalviewModel.java
test/jalview/bin/CommandLineOperations.java
test/jalview/ext/jmol/JmolCommandsTest.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AlignmentPanelTest.java
test/jalview/gui/AnnotationChooserTest.java
test/jalview/gui/AnnotationRowFilterTest.java
test/jalview/gui/JvSwingUtilsTest.java
test/jalview/gui/SeqCanvasTest.java
test/jalview/gui/SequenceRendererTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/SequenceAnnotationReportTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/renderer/OverviewResColourFinderTest.java
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
test/jalview/schemes/ClustalxColourSchemeTest.java
test/jalview/structure/StructureSelectionManagerTest.java
test/jalview/util/ColorUtilsTest.java
test/jalview/workers/AlignCalcManagerTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/sifts/SiftsClientTest.java
248 files changed:
THIRDPARTYLIBS
build.gradle
gradle.properties
help/help/help.jhm
help/help/helpTOC.xml
help/help/html/features/preferences.html
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/analysis/AAFrequency.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CrossRef.java
src/jalview/analysis/Dna.java
src/jalview/analysis/Finder.java
src/jalview/analysis/SeqsetUtils.java
src/jalview/api/AlignViewportI.java
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/AlignViewport.java
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/AnnotationPanel.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/appletgui/TreeCanvas.java
src/jalview/appletgui/js/MouseOverListener.java
src/jalview/appletgui/js/MouseOverStructureListener.java
src/jalview/bin/ApplicationSingletonProvider.java
src/jalview/bin/Cache.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewJS2.java
src/jalview/bin/JalviewLite.java
src/jalview/datamodel/Alignment.java
src/jalview/datamodel/AlignmentAnnotation.java
src/jalview/datamodel/PDBEntry.java
src/jalview/datamodel/ResidueCount.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceGroup.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/features/SequenceFeatures.java
src/jalview/ext/ensembl/EnsemblCds.java
src/jalview/ext/ensembl/EnsemblFeatures.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
src/jalview/ext/ensembl/EnsemblXref.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
src/jalview/gui/AlignExportOptions.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignViewport.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationColourChooser.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/AnnotationLabels.java
src/jalview/gui/AnnotationPanel.java
src/jalview/gui/AnnotationRowFilter.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/CalculationChooser.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/ColourMenuHelper.java
src/jalview/gui/CrossRefAction.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureEditor.java
src/jalview/gui/FeatureSettings.java
src/jalview/gui/Finder.java
src/jalview/gui/IdCanvas.java
src/jalview/gui/IdPanel.java
src/jalview/gui/JvSwingUtils.java
src/jalview/gui/OOMWarning.java
src/jalview/gui/OptsAndParamsPage.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/PCAPanel.java
src/jalview/gui/PairwiseAlignPanel.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/Preferences.java
src/jalview/gui/PromptUserConfig.java
src/jalview/gui/PymolViewer.java
src/jalview/gui/ScalePanel.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/gui/SequenceFetcher.java
src/jalview/gui/SliderPanel.java
src/jalview/gui/SlivkaPreferences.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/UserQuestionnaireCheck.java
src/jalview/gui/VamsasApplication.java
src/jalview/gui/WebserviceInfo.java
src/jalview/gui/WsJobParameters.java
src/jalview/gui/WsParamSetManager.java
src/jalview/hmmer/HMMBuild.java
src/jalview/hmmer/HMMSearch.java
src/jalview/hmmer/HmmerCommand.java
src/jalview/hmmer/JackHMMER.java
src/jalview/io/AlignFile.java
src/jalview/io/AnnotationFile.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/BackupFiles.java
src/jalview/io/BioJsHTMLOutput.java
src/jalview/io/FileFormat.java
src/jalview/io/FileFormats.java
src/jalview/io/FileLoader.java
src/jalview/io/IdentifyFile.java
src/jalview/io/ModellerDescription.java
src/jalview/io/NewickFile.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/io/VamsasAppDatastore.java
src/jalview/io/gff/InterProScanHelper.java
src/jalview/io/vamsas/Sequencemapping.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GCutAndPasteTransfer.java
src/jalview/jbgui/GDesktop.java
src/jalview/jbgui/GPreferences.java
src/jalview/project/Jalview2XML.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/schemes/ColourSchemes.java
src/jalview/schemes/JalviewColourScheme.java
src/jalview/schemes/ResidueProperties.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/urls/IdentifiersUrlProvider.java
src/jalview/util/BrowserLauncher.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/viewmodel/OverviewDimensionsShowHidden.java
src/jalview/viewmodel/ViewportRanges.java
src/jalview/workers/AlignCalcManager2.java
src/jalview/ws/AWSThread.java
src/jalview/ws/SequenceFetcher.java
src/jalview/ws/api/ServiceWithParameters.java
src/jalview/ws/dbsources/EmblFlatfileSource.java
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/dbsources/Pdb.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/gui/MsaWSThread.java
src/jalview/ws/jws1/Discoverer.java
src/jalview/ws/jws1/JPredClient.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/jws1/MsaWSThread.java
src/jalview/ws/jws1/SeqSearchWSClient.java
src/jalview/ws/jws1/SeqSearchWSThread.java
src/jalview/ws/jws2/Jws2Client.java
src/jalview/ws/jws2/Jws2ClientFactory.java
src/jalview/ws/jws2/Jws2Discoverer.java
src/jalview/ws/jws2/MsaWSClient.java
src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
src/jalview/ws/jws2/jabaws2/AADisorderClient.java
src/jalview/ws/jws2/jabaws2/JabawsServiceInstance.java
src/jalview/ws/rest/HttpResultSet.java
src/jalview/ws/rest/InputType.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJobThread.java
src/jalview/ws/sifts/SiftsClient.java
src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
src/jalview/ws/utils/UrlDownloadClient.java
src/org/json/JSONObject.java
src/swingjs/api/JSUtilI.java
test/jalview/analysis/AAFrequencyTest.java
test/jalview/analysis/AlignmentGenerator.java
test/jalview/analysis/AlignmentSorterTest.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/analysis/CrossRefTest.java
test/jalview/analysis/FinderTest.java
test/jalview/analysis/SeqsetUtilsTest.java
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
test/jalview/bin/CommandLineOperations.java
test/jalview/datamodel/AlignmentAnnotationTests.java
test/jalview/datamodel/AlignmentTest.java
test/jalview/datamodel/ResidueCountTest.java
test/jalview/datamodel/SequenceGroupTest.java
test/jalview/datamodel/SequenceTest.java
test/jalview/datamodel/features/FeatureAttributesTest.java
test/jalview/ext/ensembl/EnsemblCdnaTest.java
test/jalview/ext/ensembl/EnsemblCdsTest.java
test/jalview/ext/ensembl/EnsemblGeneTest.java
test/jalview/ext/ensembl/EnsemblGenomeTest.java
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
test/jalview/ext/jmol/JmolCommandsTest.java
test/jalview/ext/jmol/JmolParserTest.java
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
test/jalview/fts/service/pdb/PDBFTSPanelTest.java
test/jalview/gui/AlignFrameTest.java
test/jalview/gui/AlignViewportTest.java
test/jalview/gui/AlignmentPanelTest.java
test/jalview/gui/AnnotationRowFilterTest.java
test/jalview/gui/CalculationChooserTest.java
test/jalview/gui/FreeUpMemoryTest.java
test/jalview/gui/JvSwingUtilsTest.java
test/jalview/gui/PairwiseAlignmentPanelTest.java
test/jalview/gui/PopupMenuTest.java
test/jalview/gui/SeqCanvasTest.java
test/jalview/gui/SeqPanelTest.java
test/jalview/gui/StructureChooserTest.java
test/jalview/io/AnnotatedPDBFileInputTest.java
test/jalview/io/BackupFilesTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/FileFormatsTest.java
test/jalview/io/FileLoaderTest.java
test/jalview/io/FormatAdapterTest.java
test/jalview/io/Jalview2xmlBase.java
test/jalview/io/JalviewExportPropertiesTests.java
test/jalview/io/SequenceAnnotationReportTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/project/Jalview2xmlTests.java
test/jalview/renderer/OverviewResColourFinderTest.java
test/jalview/renderer/ResidueColourFinderTest.java
test/jalview/renderer/ScaleRendererTest.java
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
test/jalview/renderer/seqfeatures/FeatureRendererTest.java
test/jalview/schemes/ClustalxColourSchemeTest.java
test/jalview/schemes/ColourSchemesTest.java
test/jalview/schemes/PIDColourSchemeTest.java
test/jalview/structure/Mapping.java
test/jalview/structures/models/AAStructureBindingModelTest.java
test/jalview/util/ColorUtilsTest.java
test/jalview/util/MapListTest.java
test/jalview/util/MappingUtilsTest.java
test/jalview/util/PlatformTest.java
test/jalview/util/StringUtilsTest.java
test/jalview/ws/PDBSequenceFetcherTest.java
test/jalview/ws/dbsources/RemoteFormatTest.java
test/jalview/ws/gui/Jws2ParamView.java
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
test/jalview/ws/jabaws/RNAStructExportImport.java
test/jalview/ws/jws2/ParameterUtilsTest.java
test/jalview/ws/rest/ShmmrRSBSService.java
test/jalview/ws/sifts/SiftsClientTest.java
test/jalview/ws/utils/UrlDownloadClientTest.java
test/mc_view/PDBfileTest.java