jalview

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JAL-518 quick and dirty groovy script implementing undo/redo left justify (or right if the flag is disabled)

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    /examples/groovy/justifyRegionQuick.groovy
JAL-3516 SwingJS fix

- allows off-codebase loading of files within Info.j2sPath

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-2422 test updated

Merge branch 'feature/JAL-3551Pymol' into develop

JAL-3551 null pointer defence while structure files loading; comments

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/project/Jalview2XML.java
SwingJS update

SwingJS update

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
updated AsyncSwingWorker

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    /src/javajs/async/AsyncSwingWorker.java
AsyncFetchTask for SequenceFetcher

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    /src/jalview/gui/SequenceFetcher.java
removing debug comment

javajs.async.AsyncSwingWorker for SequenceFetcher

- set to synchronous mode for Java due to blocking on Ensembl.

- Hmm. Could be adapted to not use the Event Queue.

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    /src/jalview/gui/SequenceFetcher.java
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    /test/jalview/io/CrossRef2xmlTests.java
JSUtilI interface

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    /src/jalview/util/Platform.java
Adding SwingJS interface and utility classes

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    /src/javajs/async/Assets.java
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    /src/javajs/async/Async.java
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    /src/javajs/async/AsyncColorChooser.java
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    /src/javajs/async/AsyncDialog.java
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    /src/javajs/async/AsyncFileChooser.java
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    /src/javajs/async/AsyncSwingWorker.java
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    /src/javajs/async/SwingJSUtils.java
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    /src/swingjs/api/Interface.java
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    /src/swingjs/api/JSFileHandler.java
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    /src/swingjs/api/JSUtilI.java
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    /src/swingjs/api/js/DOMNode.java
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    /src/swingjs/api/js/HTML5Applet.java
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    /src/swingjs/api/js/HTML5AudioContext.java
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    /src/swingjs/api/js/HTML5Canvas.java
  1. … 9 more files in changeset.
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into Jalview-JS/develop

JAL-3626 transpiler and SwingJS upgrade

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9-j11/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
Varna fix for hashtable.remove(value) [unclear]

JAL-3636 ColorUtils cleaner test for hex color

SwingJS upgrade

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
MiGLayout and VARNA site zips for SwingJS 3.2.9

varna likely hashtable.remove(value) not .remove(key)

I simply made this parent.toString() to do presumably what Java would

do,

though I am not certain of that.

removing impossible test for intvervalstore containing a string

JAL-3551 corrected Pymol open session command

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-2422 correct ChimeraX save/open session commands; check for null

Merge branch 'develop' into Jalview-JS/develop

Gitter comment 2020.05.28 Cache.log.err(msg) not appearing

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    /src/jalview/javascript/log4j/Logger.java
Gitter comment 2020.05.28 Cache.log.err(msg) not appearing

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    /src/jalview/javascript/log4j/Logger.java
CR-JAL-220 JAL-3591 fixes for unlikely key value

SwingJS update

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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.7/DEV_NOTES.txt
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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.7/_j2sclasslist.txt
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    /swingjs/ver/3.2.7/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.7/timestamp
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    /swingjs/ver/3.2.8/DEV_NOTES.txt
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    /swingjs/ver/3.2.8/SwingJS-site.zip
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    /swingjs/ver/3.2.8/_j2sclasslist.txt
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    /swingjs/ver/3.2.8/net.sf.j2s.core.jar
    • -0
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    /swingjs/ver/3.2.8/timestamp
  1. … 10 more files in changeset.
JAL-3541 ensure deletion of cloverReportDir

JAL-3541 ensure deletion of cloverReportDir