jalview

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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)

    • -15
    • +55
    /src/jalview/util/ColorUtils.java
    • -13
    • +11
    /test/jalview/util/ColorUtilsTest.java
    • -1
    • +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

Commit 113cc13-2019.09.28 with added transparency fix

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

    • -0
    • +38
    /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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    • +225
    /src/jalview/io/BSMLFile.java
JAL-3453 test changes needed to allow tests to proceed unheeded by dialogs.

adding SwingJS notes for JAR file source in srcjar/

    • -0
    • +5
    /srcjar/intervalstore/README_SWINGJS.txt
    • -0
    • +6
    /srcjar/net/miginfocom/README_SWINGJS.txt
Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3459 org.json code removed

- moved to unused/

- supplied by SwingJS-site.zip

- only differences are in a few JavaScript-specific issues

- this move has NO EFFECT on the JavaScript, as SwingJS-site.zip is

unzipped last, overwriting whatever this code would have placed in

site/swingjs/j2s anyway.

    • -2411
    • +0
    /src/org/json/JSONObject.java
    • -45
    • +0
    /src/org/json/JSONPointerException.java
    • -43
    • +0
    /src/org/json/JSONPropertyIgnore.java
    • -47
    • +0
    /src/org/json/JSONPropertyName.java
  1. … 55 more files in changeset.
JAL-3210 Just about working transpilation. Some work needed for new Java 11 classes

    • -0
    • +32
    /utils/jalviewjs/template.html
    • binary
    /utils/testlibs/classgraph-4.1.6.jar
JAL-3066 Create labels for fields and hack it to work with multiple valued parameters

    • -2
    • +2
    /src/jalview/gui/OptsAndParamsPage.java
    • -2
    • +16
    /src/jalview/ws/params/simple/BooleanOption.java
    • -0
    • +16
    /src/jalview/ws/params/simple/Option.java
    • -16
    • +29
    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3261 no save in setColourPropertyNoSave !

JAL-3261 tidy up get/set properties in Cache, Javadoc, tests

    • -1
    • +1
    /src/jalview/gui/ColourMenuHelper.java
JAL-3458 redraw alignment and Overview on Cancel in Feature Settings

    • -9
    • +39
    /src/jalview/gui/FeatureSettings.java
Merge remote-tracking branch 'origin/tasks/JAL-3070_wsinterfaces' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3066 change service type naming to avoid menu entry duplication.

Merge branch 'develop' into documentation/JAL-3407_2.11.1_release

Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3070 set calcId and autocalculated flags for annotation returned by the service