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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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Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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JAL-2349 JAL-3855 highlight residues associated with elements under mouse - Jmol doesn’t like highlighting many residues at once this way.

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JAL-2349 JAL-3855 experiment masking hidden columns in contact matrix

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

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JAL-2349 avoid div-by-zero when annotation height is zero (though poss better to simply avoid rendering contact at all)

JAL-2349 JAL-3855 adapt renderer for AlignmentI.getContactList(..) mapping to sequence associated reference frame

JAL-4033 fix drag selections and distinguish row/columnwise highlights from intersections on matrix

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JAL-3855 RGB colours from the alphafold paE scale.

JAL-2349 JAL-4033 refactored contact matrix geom calc to allow reporting of mapped positions in tooltip

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    ./ContactGeometry.java
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JAL-2349 JAL-3855 column selection highlighting

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JAL-3855 2349 TODO

JAL-4071 first working prototype

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Merge branch 'bug/JAL-3612_overviewFeatureOrdering' into develop

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JAL-2349 JAL-3855 formatting

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JAL-4033 TODO re highlighting current column selection

JAL-2349 debugged and simplified (a little) the scaled rendering of contact maps - still got a rounding error somewhere !

JAL-2349 JAL-3855 resolve sequence position for contact lookup and catch out bound contact requests

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

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JAL-3438 spotless for 2.11.2.0

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    ./seqfeatures/FeatureRenderer.java
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JAL-3438 - all src and test run through spotless..

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    ./seqfeatures/FeatureRenderer.java
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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855 combined new logic for 2.11.2 3d-beacons with original hack to resolve PAE and CIF Conflicts: src/jalview/ws/dbsources/EBIAlfaFold.java

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JAL-3079 JAL-3055 remember to reset font transform after rendering logo

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
JAL-2349 - deobfuscate the renderer and fix it .. work in progress

Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112

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JAL-3612 use _last_ drawn colour per feature type in Overview

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