jalview

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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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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
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JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/differences.txt
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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.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

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

JAL-3690 patch out spinning animation for web service jobs

JAL-3690 disable proxy server for JalviewJS

JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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    /src/jalview/analysis/AlignmentSorter.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/TitledPanel.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/JvSwingUtils.java
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    /src/jalview/gui/OverviewPanel.java
  1. … 42 more files in changeset.