jalview

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Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

JAL-3690 Fixed slivka wsmenu categories.

JAL-3690 Fixed slivka wsmenu categories.

JAL-3796 update signature for uninstaller on OSX

JAL-3796 update to Install4j 8.0.10 and add config for code notarization

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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  1. … 24 more files in changeset.
JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/differences.txt
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  1. … 32 more files in changeset.
JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/ViewSelectionMenu.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3419 improved look of tabs

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

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    /test/jalview/datamodel/SequenceTest.java
JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

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    /test/jalview/datamodel/SequenceTest.java
JAL-3416 Added FlatLightLaf, use with -Dlaf=flat property

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    /j11lib/flatlaf-0.46.jar
JAL-3788 synchronize concurrent findColour() and alignmentChanged()

JAL-3788 synchronize concurrent findColour() and alignmentChanged()

JAL-3761 more consistent parameter naming

JAL-3761 more consistent parameter naming

JAL-3790 New getdown version and jar files

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    /getdown/lib/getdown-launcher-local.jar
JAL-3790 Enable copy to clipboard when mouse click on the getdown splashscreen StatusPanel

JAL-3789 tidied net.sf.j2s.core.Java2ScriptCompiler code for submission

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    /Java2ScriptCompilationParticipant.java
JAL-3789 Removed debugging printlns

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    /Java2ScriptCompilationParticipant.java
JAL-3789 First attempt for configurable property to look at

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    /Java2ScriptCompilationParticipant.java
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    /Java2ScriptCompiler.java
JAL-1713 restore project with no Overview, regardless of Preferences

JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.

JAL-1713 close and replace auto-opened Overview with restored Overview

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/project/Jalview2XML.java
JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)

JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites