jalview

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

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    /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()

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    /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.

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /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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    /src/jalview/gui/AlignFrame.java
JAL-3436 move/rename/private fields refactoring only

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    /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

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

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    /utils/jalviewjs/Java2ScriptCompilationParticipant.java
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    /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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    /test/jalview/util/StringUtilsTest.java
JAL-3210 Added site transfer dir. New net.sf.j2s.core.jar ONLY WORKS WITH ECLIPSE 2019-09+

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    /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

Commit 113cc13-2019.09.28 with added transparency fix

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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
JAL-3407 update release date for Jalview 2.11.1

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    /README_GRADLE_JALVIEWJS-2019-10-15.md
JAL-3368 retaining branch for future SwingJS reference

JAL-3437 Desktop File...Load Project fails in JalviewJS

- just needed to use the File object rather than the file name in the

call to Jalview2XML.loadJalviewAlign

JAL-3445 branch for BSML file reading development

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    /src/jalview/io/BSMLFile.java
JAL-3453 test changes needed to allow tests to proceed unheeded by dialogs.