jalview

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JAL-3436 fix for reload not reloading files

-- fix for Jalview projects reload where reload was using just the file

name.

-- will test further to ensure this is only in relation to JVP files

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    /src/jalview/project/Jalview2XML.java
JAL-3210 replacing j11lib/Jmol-14.29.17-no_netscape.jar with unsigned version. Temporary fix

    • binary
    /j11lib/Jmol-14.29.17-no_netscape.jar
JAL-3210 removed netscape.javascript objects from Jmol-14.29.17.jar to avoid blocking Java 11 clash with jdk.jsobject Java 11 module

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    /j11lib/Jmol-14.29.17-no_netscape.jar
JAL-3210 removed eclipse project, classpath and core settings files from branch. Now generate these (once only) with 'gradle eclipse'.

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    /.settings/org.eclipse.jdt.core.prefs
JAL-3436 debug comments out in JSPopupMenuUI.js

    • binary
    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3453

test to see if the build testing passes this test.

Slight modifications from Mungo's last commit to account for recent

changes in public/private fields, but that is all.

Passing tests on Bob's Windows machine.

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    /test/jalview/gui/AlignFrameTest.java
Merge branch 'develop' into Jalview-JS/develop

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/analysis/CrossRef.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/PopupMenu.java

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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/AnnotationExporter.java
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    /src/jalview/gui/FeatureSettings.java
  1. … 19 more files in changeset.
Jal-3066 Retrieve job log and error log from the server.

JAL-3066 AACon: pass the instance name of the service to the alignment analysis UI

JAL-3066 Check if annotation and features are present before fetching

Merge remote-tracking branch 'origin/tasks/JAL-3070_wsinterfaces' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3066 report job ID when submitted

JAL-3066 debug info: check response when adding features and annotation

JAL-3066 JAL-3070 AACon: pass the name of the service to the alignment analysis UI

JAL-3066 hack to instantiate the correct client according to slivka service annotation. NEEDS ROBUST TESTING!

JAL-3070 jaba/slivka independent tests for disorder and AACon services

JAL-3070 JAL-3066 provide standard concrete instances for instantaneous analysis UI settings container

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    /src/jalview/ws/jws2/Jws2ClientFactory.java
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    /src/jalview/ws/params/AutoCalcSetting.java
JAL-3070 JAL-3066 fix initialisation of slivka ServiceWithParameters

Revert "JAL-3070 JAL-3066 fix initialisation of slivka ServiceWithParameters"

This reverts commit daa1765ab2101480a724b92a3f3e7dee662ba943.

JAL-3070 use identity equivalence for workers rather than relying on equals not being overridden to detect their presence.

JAL-3070 formatting

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    /src/jalview/ws/jws2/ParameterUtils.java
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.

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    /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