jalview

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JAL-3463 SwingJS-site.zip update for Thread.sleep()

- throws InterruptedException if called in JavaScript

    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3210 Better integration with Eclipse as IDE. FIXED THE TEST JAR ATTRIBUTE, HOORAH

    • -1
    • +22
    /README_GRADLE_JALVIEWJS-2019-10-22.md
JAL-3423 more System.lineSeparator() in place of \n

    • -9
    • +9
    /test/jalview/analysis/TestAlignSeq.java
    • -2
    • +5
    /test/jalview/math/RotatableMatrixTest.java
JAL-3423 test coverage

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    • +1
    /test/jalview/datamodel/PDBEntryTest.java
JAL-3253 rename method, add Javadoc

JAL-3423 use System.lineSeparator() in code and tests

    • -11
    • +9
    /src/jalview/analysis/AlignSeq.java
JAL-32423 tidying

    • -6
    • +6
    /test/jalview/gui/AlignViewportTest.java
    • -5
    • +5
    /test/jalview/gui/AlignmentPanelTest.java
    • -17
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    /test/jalview/gui/SeqCanvasTest.java
    • -13
    • +0
    /test/jalview/gui/SeqPanelTest.java
JAL-3210 small fix for jalviewjsBuildDir

JAL-3210 project name explicitly set. updated README_GRADLE_JALVIEWJS...md file. fixed eclipseRootDir detection for macos.

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    • +0
    /README_GRADLE_JALVIEWJS-2019-10-15.md
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    /README_GRADLE_JALVIEWJS-2019-10-22.md
JAL-3210 added absolute path for transpile log

JAL-3210 Improved/fixed the tempdir creation/storage for eclipse workspace

JAL-3210 Different j2s plugin for different versions of eclipse. Not great, but good for now

JAL-3210 Changed eclipse workspace dir to be a system temp dir [held in build/jalviewjs/eclipse_workspace_location] that persists until a gradle clean

JAL-3463 Thread.sleep()

setting sleep() to throw InterruptedException()

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3416 first attemp at using com.sun.java.swing.plaf.gtk.GTKLookAndFeel in Linux/solaris. Some issues

JAL-3463 alert for Thread.sleep; JAL-3378 java.util.logging.Logger implemented.

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3066 Slivka client update for changed api endpoints.

JAL-3436 null large object reference, tidy method visibility

JAL-3436 save filePath from fileObject, tidy updateRecentlyOpened

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    • +64
    /src/jalview/gui/AlignFrame.java
JAL-3436 move/rename/private fields refactoring only

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    • +61
    /src/jalview/project/Jalview2XML.java
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3436 broken reader - SwingJS issue (wrong JAL number in last commit)

- java.util.logging.Logger not fully implemented.

- this fix just removes Logger calls from javax.xml classes.

- see JAL-3461 for full fix TODO

JAL-3261 broken reader - SwingJS issue

- java.util.logging.Logger not fully implemented.

- this fix just removes Logger calls from javax.xml classes.

- see JAL-3461 for full fix TODO

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3210 changed classes for net.sf.j2s.core

    • -0
    • +185
    /utils/jalviewjs/Java2ScriptCompilationParticipant.java
    • -0
    • +586
    /utils/jalviewjs/Java2ScriptCompiler.java
Merge branch 'Jalview-jJS/JAL-3253-applet-JAL-3436' into Jalview-JS/JAL-3253-applet

JAL-3368 'web' colour parsing reinstated (for now)

JAL-3368 removed parsing web colours (now on a separate branch)

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    /src/jalview/util/ColorUtils.java
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    /test/jalview/util/ColorUtilsTest.java
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    • +19
    /test/jalview/util/StringUtilsTest.java
JAL-3210 Added site transfer dir. New net.sf.j2s.core.jar ONLY WORKS WITH ECLIPSE 2019-09+

    • binary
    /utils/jalviewjs/eclipse/dropins/net.sf.j2s.core_3.2.4.jar
Merge branch 'Jalview-JS/develop' into Jalview-JS/develop_with_gradle_build

Merging in Jalview-JS/develop (should be no changes -- just checking)

JAL-3442 (Aug 28 commit) option to use/not use cache