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Merge branch 'develop' into merged_2_11_2_0_to_2_12 updates JAL-3362 2.12 alpha with 2.11.2.5 release changes. Still has failing tests. 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/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

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    ./features/SequenceFeatures.java
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Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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JAL-2349 allow contact matrix to provide labels for its annotation row

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JAL-4033 - heuristic threshold for pAE matrix - mark any column where pAE values for column+8.. lie outside threshold - definitely better to do a watershed or other type of clustering

JAL-2349 formatting/pick correct exception

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JAL-2349 JAL-3855 off by one and daft return

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JAL-2349 JAL-3855 ContactListI.getPosition() to recover original position passed to ContactMatrixI.getContactListFor(..)

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JAL-2349 JAL-3855 experimenting with filtering columns based on mean of contact map range

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JAL-3855 JAL-2349 AlignmentI.getContactList takes care of mapping columns to sequence positions for sequence associated contact matrices. Need to map selected positions back for drag selects

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JAL-2349 adjusted range calculation to be inclusive rather than inclusive, exclusive of bounds

JAL-2349 JAL-3855 column selection highlighting

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JAL-1551 formatting

JAL-2349 JAL-3855 Integrate pAE retrieval in StructureFile so it can be transferred as reference annotation

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JAL-2349 reusable contact map holder for SequenceI and AnnotatedCollectionI

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    ./ContactMapHolder.java
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    ./ContactMapHolderI.java
JAL-1551 formatting

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    ./annotations/AlphaFoldAnnotationRowBuilder.java
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    ./annotations/AnnotationRowBuilder.java
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JAL-3895 alphafold colours via pluggable annotation row builder. Also ensures min/max set correctly

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    ./annotations/AlphaFoldAnnotationRowBuilder.java
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    ./annotations/AnnotationRowBuilder.java
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Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppred_calcs

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JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequences() to clipboard

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JAL-4028 experiment - THISISAPLACEHOLDER sequences get additional sequence data (as ‘X’) to cover the extent of features on the sequence.

JAL-4027 getter for contact matrices on the Alignment.

JAL-1551 formatting

Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

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JAL-4023 store distances as doubles

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JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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JAL-3878 Add char[] constructor to Sequence

JAL-3860 prototype for highlight species/assembly/chromosome/position

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JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

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JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

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    ./GenomicAssemblies.java
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JAL-3746 apply copyright to source

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