jalview

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JAL-3444 translucent overview

- oops, that broke Java!

JAL-3444 translucent overview

- was missing 2nd isJS block

- JS was setting pixel background to white instead of defaultColour

prior to transparent color painting

JAL-3456 re-use of existing jar files

  1. … 866 more files in changeset.
JAL-3456 Some task improvements for use in Eclipse as IDE

JAL-3456 Some task improvements for use in Eclipse as IDE

JAL-3066 Read parameters directly from args list allowing for multiple values.

Update slivka-client library: multiple form field values.

JAL-3066 Fix log files retrieval.

JAL-3456 fixed some backticks in README.md

JAL-3210 JAL-3456 Mothballing work done on using goomph for jalviewjs build

JAL-3210 JAL-3456 Mothballing work done on using goomph for jalviewjs build

    • -0
    • +2
    /TODO/org.eclipse.jdt.launching.prefs
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

    • -2
    • +14
    /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

    • binary
    /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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    • +1
    /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
    • -2
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    /src/jalview/gui/AlignmentPanel.java
    • -48
    • +139
    /src/jalview/gui/AnnotationExporter.java
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    • +102
    /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
    • -3
    • +29
    /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.