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

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JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.

JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.

JAL-4026 more pointless sleeps

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JAL-4026 isolate the failing test in its own class

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    ./SeqPanelTest_isolate.java
JAL-4026 make jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence sequential

JAL-1953 2.11.2 with Archeopteryx! Minimal patches and Merge branch 'kjvdh/features/PhylogenyViewer' into merge/2_11_2/PhylogenyViewer also restored last kjvdh build of forester to j8 and j11lib directories Conflicts: .classpath j8lib/forester.jar resources/lang/Messages.properties src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/project/Jalview2XML.java src/jalview/schemabinding/version2/JalviewModelSequence.java src/jalview/util/DBRefUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/jalviewjs/buildxml/build.xml

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Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh/features/PhylogenyViewer_tabbedsupport Update from Release 2.11.2 develop branch JAL-1953 Conflicts: .classpath .project resources/lang/Messages.properties src/jalview/bin/Jalview.java src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/CalculationChooser.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/gui/TreePanel.java src/jalview/gui/WebserviceInfo.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/io/NewickFile.java src/jalview/math/Matrix.java src/jalview/math/MatrixI.java src/jalview/util/MappingUtils.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/eclipse/org.eclipse.jdt.core.jalview.prefs utils/eclipse/org.eclipse.jdt.ui.prefs

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JAL-3990 gradle spotlessApply

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3085 update tests and mock responses, new P0dtd1 testcase

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    ./structurechooser/StructureChooserQuerySourceTest.java
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Merge branch 'master' into releases/Release_2_11_2_Branch

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JAL-3746 apply copyright to tests

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JAL-3438 spotless for 2.11.2.0

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JAL-3438 - all src and test run through spotless..

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JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

Conflicts:

src/jalview/bin/Jalview.java

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JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

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JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality

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JAL-3829 parallel not welcome here

JAL-3829 test flakiness and human flakiness

JAL-3829 more info on test fail - seems to be flaky

JAL-3829 move mock query and responses to files

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3829 ensure unmock the FTS PDB and TDB clients after mocking for a test

JAL-3829 minimal test of additional TDB filters - not at all robust

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    ./structurechooser/StructureChooserQuerySourceTest.java
JAL-3829 ensure tests use mocked service - proper exception for mocked 400 response

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JAL-3829 patch failing tests and todo for future

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3829 insert title for structures from PDBe

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3829 allow client-side selection of structures for a sequence by passing in discovered structures

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3829 work in progress - look up additional metadata from PDBe for structures discovered via TDBFTS

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    ./structurechooser/StructureChooserQuerySourceTest.java
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JAL-3829 pull out structure chooser query source tests to new class

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    ./structurechooser/StructureChooserQuerySourceTest.java