jalview

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JAL-3446 separated out potential exceptions for simplified key mask operation

JAL-3446 test for simpler key mask operation

JAL-3446 test for simpler key mask operation

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    /src/jalview/jbgui/GAlignFrame.java
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    /src/jalview/jbgui/GCutAndPasteTransfer.java
JAL-3446 JAL-3253 Preferences

- unnecessary static initialization of StructureViewer

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    /src/jalview/jbgui/GPreferences.java
JAL-3446 from JAL-3253-applet StockholmFile updated to 26b115b (gmungoc)

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    /src/jalview/io/StockholmFile.java
helpful hints from Ben

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    /swingjs/README-JALVIEW
JAL-3446 latest jmol zip from JAL-3253-applet (commit c28e0a1)

    • binary
    /utils/jalviewjs/libjs/jmol-app.zip
JAL-3446 fix broken test

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    /test/jalview/util/ColorUtilsTest.java
Bob's gitignore addition

/build-site.xml

/buildcore.xml

/j11lib/intervalstore-v1.0.jar

JAL-3626 from JAL-3253-applet Jalview.java

adds JalviewLite interface; removes deprecated AppletContext interface

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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignViewport.java
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    /src/jalview/gui/Preferences.java
JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

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    /test/jalview/analysis/FinderTest.java
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    /test/jalview/ext/jmol/JmolParserTest.java
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    /test/jalview/gui/AlignViewportTest.java
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    /test/jalview/gui/AlignmentPanelTest.java
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    /test/jalview/gui/AnnotationChooserTest.java
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    /test/jalview/gui/CalculationChooserTest.java
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    /test/jalview/gui/FreeUpMemoryTest.java
  1. … 3 more files in changeset.
JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/Preferences.java
JAL-3626 from JAL-3253-applet web page embedding

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    /src/jalview/bin/Jalview.java
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    /src/jalview/bin/JalviewAppLoader.java
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    /src/jalview/gui/OverviewPanel.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3626 from JAL-3253-applet JalviewLite scrollTo capability

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    /src/jalview/gui/AlignmentPanel.java
JAL-3626 from JAL-3253-applet CalculationChooser

-- dissociated from panel for static access by JavaScript

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    /src/jalview/gui/CalculationChooser.java
JAL-3626 from JAL-3253-applet StructureViewer/Chooser

-- disassociates viewer launch from chooser

-- for JavaScript interface

(sorry about JAL-3262 ref previously)

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/StructureViewer.java
JAL-3262 from JAL-3253-applet temp. Desktop instance hack

JAL-3262 from JAL-3253-applet JalviewApp integration

JAL-3262 from JAL-3253-applet JalviewApp integration

JAL-3262 from JAL-3253-applet AppletParams + Cache.setPropertyNoSave

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    /src/jalview/bin/AppletParams.java
JAL-3262 from JAL-3253-applet ArgsParser

JAL-3262 from JAL-3253-applet Platform JS interface upgrade

JAL-3262 from JAL-3253-applet Preferences final static String upgrade

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    /src/jalview/gui/Preferences.java
JAL-3262 from JAL-3523-applet JalviewApp and JalviewJSApi

- removes JaliewJSLite dependence

- removes AlignFrameI reference

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    /src/jalview/api/JalviewApp.java
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    /src/jalview/bin/JalviewJSApi.java
JAL-3262 from JAL3253-applet core_jvjmol.z.js static load

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    /src/jalview/gui/StructureViewer.java
JAL-3626 Regex optimization from JAL-3253-applet; also minor StockholmFile for loop opt.

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    /src/jalview/ext/ensembl/EnsemblCdna.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblProtein.java
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    /src/jalview/io/ModellerDescription.java
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    /src/jalview/io/NewickFile.java
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    /src/jalview/io/StockholmFile.java
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    /src/jalview/ws/dbsources/EmblCdsSource.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/Uniprot.java
THIRDPARTYLIBS referred to intervalstore-v1.0 still

corrects Platform.openURL

JAL-3626 adding compatible Platform.java

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    /src/jalview/util/Platform.java
SwingJS update

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    /src/swingjs/api/js/README.txt
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip