jalview

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JAL-3453 Some tests require different Desktop constructor

even better, simpler idea:

static boolean instanceOnly

public static Desktop getInstanceOnly()

{

instanceOnly = true;

return getInstance();

}

JAL-3453 Some tests require different Desktop constructor

better idea:

Desktop.getInstanceOnly()

- creates an instance with no dialog prompting and no frame display,

similar to headless mode, but not fully bypassing the code that

Jalview.headless bypasses.

JAL-3453 better JavaDoc

JAL-2114 just noting where the exo-location error presents itself.

    • -1
    • +2
    /src/jalview/ws/dbsources/EmblXmlSource.java
JAL-3454 file loading string-only (testNG) fails for PDB file

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    /src/jalview/io/AppletFormatAdapter.java
JAL-3453 Some tests require different Desktop constructor

JAL-3451 setting dimensions for AlignFrame if embedded

JAL-3451 updated SwingJS-site.zip

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
updated _j2sclasslist.txt and _j2sclasslist_jmol.txt

JAL-3451 JalviewJS embedded mode not resizing

- adds Platform.getDimIfEmbedded(frame, defaultWidth, defaultHeight)

- implemented for AlignFrame, TreePanel, and PCAPanel

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    /site-resources/jalview_embedded_example1.html
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    /src/jalview/bin/Jalview.java
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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

Desktop JavaDoc comments for Mungo from gitter discussion

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    /src/jalview/gui/Desktop.java
JAL-3451 older embedding test html removed

Current test is site/jalview_embedded_example1.html

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    /site-resources/jalview_bin_JalviewJS_embedded.html
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    /site-resources/jalview_bin_JalviewJS_embedded_core.html
JAL-3210. IT LIVES\! some goomph transpilation going on

JAL-3210 ... a bit closer ... goomph jalviewjs build

    • binary
    /gradle/plugins/com.seeq.eclipse.importprojects-1.4.0.jar
    • binary
    /gradle/plugins/net.sf.j2s.core-3.2.4.jar
Merge remote-tracking branch 'origin/tasks/JAL-3070_wsinterfaces' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3253 miscellaneous tidying up before merge to JS-develop

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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/OverviewPanel.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/urls/IdentifiersUrlProvider.java
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    /src/jalview/ws/sifts/SiftsClient.java
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    /src/jalview/ws/sifts/SiftsSettings.java
JAL-3253 extract methods for getConservation/PIDSlider

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    /src/jalview/gui/SliderPanel.java
JAL-3345 small simplification

JAL-3210 ... almost goomph build

JAL-3210 Almost working goomph build

  1. … 863 more files in changeset.
JAL-3070 reinstate the internal test service URL for Slivka-bio

JAL-3070 test jabaws and slivka AACon service functionality

JAL-3070 slivka service discovery as a background thread - still need to unify Jabaws & slivka discoverer patterns

JAL-3070 basic AACon service functionality test

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    • +198
    /test/jalview/ws/jabaws/AAConAnnotAndSettingsIO.java
JAL-3070 alignment analysis service worker UI and settings management refactored from Jws2/JABAWS specific classes

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    /src/jalview/ws/jws2/Jws2ClientFactory.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
    • -0
    • +396
    /src/jalview/ws/jws2/PreferredServiceRegistry.java
JAL-3070 call checkDone() ASAP to avoid race condition for threads watching state of the calculation manager (e.g. in tests)

JAL-3383 tidy method signature and Javadoc

JAL-3253 one global singleton instance of EnsemblInfo suffices

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    /src/jalview/ext/ensembl/EnsemblInfo.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
JAL-3383 code and unit test tweaks