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