jalview

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SwingJS runtime update 3.2.9-v1b

- mostly fixes from recent SwingJS work involving

-- expanded FileSystem and temp file management

-- super-fast HashMap (faster than Java!), HashTable,

StringBuilder, StringBuffer, NumberFormat, DecimalFormat

-- improved ResourceBundle

-- full Locale information

-- additional BufferedImage/ColorModel/Raster support

- fixes temp files not cached (JSTempFile, for Jmol)

- fixes AbstractStringBuilder.replace() typo

- reverts recent HashSet acceleration due to Jalview

using String.hashCode() for display order of features

    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
JAL-3560 moving JS-specific code to Platform, fix Platform.streamToFile

JAL-3560 better build xml names

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    /build-2-core.xml
JAL-3541 increase maxheapsize for test worker process

JAL-3541 increase maxheapsize for test worker process

JAL-3541 tidying build.gradle, delete cloverInstrDir re-added

JAL-3541 tidying build.gradle, delete cloverInstrDir re-added

JAL-3305 don't propagate an empty SelectionGroup to complement view

JAL-3541 put org.gradle.jvmargs explicitly into gradle.properties

jmol.app.zip and SwingJS-site.zip; java2script 3.2.9-v1b

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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
  1. … 8 more files in changeset.
Java 11/Gradle 2.5 upgrade

    • binary
    /j11lib/FastInfoset.jar
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    /j11lib/JGoogleAnalytics_0.3.jar
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    /j11lib/Jmol-14.29.17-no_netscape.jar
    • binary
    /j11lib/VARNAv3-93.jar
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    /j11lib/VAqua5-patch.jar
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    /j11lib/apache-mime4j-0.6.jar
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    /j11lib/biojava-core-4.1.0.jar
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    /j11lib/biojava-ontology-4.1.0.jar
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    /j11lib/commons-codec-1.3.jar
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    /j11lib/commons-compress-1.18.jar
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    /j11lib/commons-discovery.jar
  1. … 81 more files in changeset.
JAL-3559 temporary branch adding JS files complete

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    /.settings/org.eclipse.wst.jsdt.ui.superType.container
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    /.settings/org.eclipse.wst.jsdt.ui.superType.name
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    /build.Bob-Windows.xml
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    /libjs/MiGLayout-site.zip
    • binary
    /libjs/VARNA-site.zip
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    /libjs/intervalstore-site.zip
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    /site-resources/applets-nocore.html
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    /site-resources/applets.html
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    /site-resources/css/ie6.css
  1. … 76 more files in changeset.
JAL-3541 merged cleanClover with develop

old JavaScript debug var removed -- JavaScript only

JalviewJS2 addition

JAL-3541 perhaps a better clean for clover. fixed

JAL-3541 perhaps a better clean for clover. fixed

JAL-3541 perhaps a better clean for clover

JAL-3541 perhaps a better clean for clover

JAL-3560 fixes _j2sclasslist.txt

transpiler 3.9.1 is NOT backward compatible. It corrects an earlier

implementation of generic class method references. So everything does

need rebuilding.

Jmol isn't rebuilt yet.

updated interval-site.zip

returning src2 -> srcjar

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    /src2/fr/orsay/lri/varna/README_SWINGJS.txt
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    /src2/fr/orsay/lri/varna/VARNA.java
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    /src2/fr/orsay/lri/varna/VARNAPanel.java
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    /src2/fr/orsay/lri/varna/applications/BasicINI.java
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    /src2/fr/orsay/lri/varna/applications/VARNAGUI.java
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Java 11 integration;

-- compiler complaining about javax.xml module

Failed to resolve resource /.build_properties:

@swingjs/j2s/jalview/bin/Cache.js:164:24

transpiler was 3.2.9-v1 now 3.2.4.07 for net.miginfocom.swing.MigLayout

TypeError: C$.UNIT_MAP.put$TK$TV is not a function

-- some runtime errors involving resources

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    /.settings/org.eclipse.jdt.core.prefs
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    /j11lib/FastInfoset.jar
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    /j11lib/JGoogleAnalytics_0.3.jar
    • binary
    /j11lib/Jmol-14.29.17-no_netscape.jar
    • binary
    /j11lib/VARNAv3-93.jar
    • binary
    /j11lib/VAqua5-patch.jar
    • binary
    /j11lib/apache-mime4j-0.6.jar
    • binary
    /j11lib/biojava-core-4.1.0.jar
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    /j11lib/biojava-ontology-4.1.0.jar
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    /j11lib/commons-codec-1.3.jar
    • binary
    /j11lib/commons-compress-1.18.jar
  1. … 445 more files in changeset.
JAL-3541 rejigged clover tasks very mildly

JAL-3541 rejigged clover tasks very mildly

Revert "JAL-3541 trying out previous cloverReport task"

This reverts commit dc70a1f7934471a4084c3f10e7bd630d72aa3bf3.

JAL-3541 trying out previous cloverReport task

JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings for linked cds/protein views

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    /help/help/html/features/linkedfeatsettings.png
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    /help/help/html/features/splitView.html
JAL-3407 JAL-3549 explicitly mention the ‘no features’ dialog, and how an existing selection affects the sort alignment by feature score/density

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    /help/help/html/features/featuresettings.html
JAL-3407 group together ‘virtual feature’ related features in release notes