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JAL-1988 Added a saves in progress check for quit

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JAL-1988 added a saveInProgress stack to BackupFiles

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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-1953 JAL-2889 don’t read additional lines when looking for phyloxml header

JAL-4021 todo & fix FileFormat tests

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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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JAL-3288 Replace all javax.swing.JInternalFrame with extended jalview.jbgui.ClassicJInternalFrame

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JAL-3365 per-sequence secondary structure symbol ‘X’ is not properly exported and reimported

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

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JAL-3981 patch tests and remove errant imports

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JAL-3990 gradle spotlessApply

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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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JAL-3980 defensive copy - inefficient but fixes bug

JAL-3981 Additional line breaks - sort of helps

JAL-3981 strategic newlines to help speed up Java's html parser

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JAL-3746 apply copyright to source

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JAL-3438 spotless for 2.11.2.0

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JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2

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

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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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Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

That looks good. I was almost going to do something similar (I was thinking jalview.log.Log, but jalview.bin.Console is just as good) so happy with this!

That looks good. I was almost going to do something similar (I was thinking jalview.log.Log, but jalview.bin.Console is just as good) so happy with this!

Added those in. I'm still converting to String with getCanonicalName in the getLogger(Class ...) method because, e.g. JLogger jlogger1 = JLogger.getLogger(Jalview.class); JLogger jlogger2 = JLogger...

Added those in. I'm still converting to String with getCanonicalName in the getLogger(Class ...) method because, e.g.
JLogger jlogger1 = JLogger.getLogger(Jalview.class);
JLogger jlogger2 = JLogger.getLogger("jalview.bin.Jalview");
should really return an existing logger in the registry if it exists, and the String name is the registry key.

Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' of https://source.jalview.org/git/jalview into update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more

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JLogger loglevel check on whether to call the actual logger or not. New factory methods with Class.

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