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JAL-4046 JAL-3993 imports reformatting

JAL-4046 JAL-3993 patch for 2.11.2.4 release

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Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop

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JAL-4034 show the loading spinner when switching between tabs

JAL-4055 quick patch to see how Jalview looks as a free-floating multiwindowed app rather than a Desktop contained app

JAL-4048 fix disappearing sequence IDs, and non-positional feature descriptions

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JAL-4047 - proof of concept for JAL-4048 - display columns of info in sequence ID panel.

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JAL-4045 - don't apply distribution dependent scale factor to the axis lines!

JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can moveToFront. Minor improvement to Search 3DB button appearance

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JAL-4034 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (similar to JalviewJS)

JAL-4041 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can be raised.

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JAL-4041 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (like JavliewJS)

JAL-4034 change to jalview property name

JAL-4034 showConfirmDialog works for both desktop and jalviewjs

JAL-4034 Non-blocking 3D Beacons query after warning dialog

JAL-4034 allow a jalview_property to set the threshold level

JAL-4034 fix #3 change uniprot ref fetch dialog to a ‘warning’ shown when many ids have to be retrieved

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JAL-4034 Fix #2 show an icon and a button to press to initiate search

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JAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop. Use result to not add About and Preferences to normal menus.

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JAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system to set APQhandler for both J9+ and now Java 8

JAL-2349 JAL-4027 JAL-3855 quick hack to add contact matrices accompanying alignment objects via sequence fetcher or imported from other sources

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

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JAL-4026 update the viewport’s wrapped width after calculating it

JAL-4026 update the viewport’s wrapped width after calculating it

JAL-4026 more pointless sleeps

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JAL-4024 only render partially when new view overlaps with last rendered annotation panel view

JAL-4023 use %g for distances (scientific notation for very small or large values)

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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minimal fixes - probably not valid since forester jar out of sync

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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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