jalview

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Merge branch 'alpha/merge_212_JalviewJS_2112' into spike/JAL-3622_Scanner_swingjs_J212_merge

Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJS_2112

Conflicts:

src/jalview/gui/Desktop.java

src/jalview/gui/Preferences.java

src/jalview/jbgui/GPreferences.java

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-3683 retrieve job status to output stream

JAL-6386 update slivka client for j2s compatibility

JAL-3622 update with swingJS from hansonr1

    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/SwingJS-site.zip
    • binary
    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/AlignViewportI.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/Sequence.java

src/jalview/datamodel/SequenceI.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/JvSwingUtils.java

src/jalview/gui/OverviewPanel.java

src/jalview/gui/PopupMenu.java

src/jalview/gui/SplitFrame.java

src/jalview/gui/WsJobParameters.java

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/FileLoader.java

src/jalview/io/StockholmFile.java

src/jalview/jbgui/GAlignFrame.java

src/jalview/jbgui/GPreferences.java

src/jalview/renderer/AnnotationRenderer.java

src/jalview/viewmodel/AlignmentViewport.java

src/jalview/ws/jws2/Jws2Discoverer.java

test/jalview/analysis/AAFrequencyTest.java

test/jalview/gui/AlignFrameTest.java

test/jalview/gui/AlignViewportTest.java

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/appletgui/AlignFrame.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/appletgui/TitledPanel.java
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    /src/jalview/datamodel/Alignment.java
  1. … 60 more files in changeset.
JAL-3529 test updated for revised signature of getDBRefs()

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    /test/jalview/io/StockholmFileTest.java
Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/ext/ensembl/EnsemblInfo.java
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    /src/jalview/ext/ensembl/EnsemblMap.java
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    /src/jalview/gui/IdPanel.java
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    /src/jalview/gui/PopupMenu.java
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    /src/jalview/gui/SeqPanel.java
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    /src/jalview/io/StockholmFile.java
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    /src/jalview/util/DBRefUtils.java
  1. … 5 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
JAL-3613 remove debug code committed in error

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    /src/jalview/util/BrowserLauncher.java
JAL-3613 check sequence overlap when matching search results

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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/util/BrowserLauncher.java
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

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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/gui/AnnotationLabels.java
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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/CalculationChooser.java
  1. … 28 more files in changeset.
Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalview_212_alpha

JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used

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    /utils/eclipse/org.eclipse.jdt.ui.prefs
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop

JAL-3407 add GPL license to Jalview source files

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    /src/jalview/analysis/GeneticCodeI.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/bin/JalviewTaskbar.java
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    /src/jalview/bin/MemorySetting.java
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    /src/jalview/datamodel/GeneLociI.java
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    /src/jalview/datamodel/GeneLocus.java
  1. … 29 more files in changeset.
JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera

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

JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0

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

JAL-3574 JAL-3407 release notes

Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release

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

JAL-3407 add and document ComputePeptideVariants.groovy

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    /examples/groovy/ComputePeptideVariants.groovy
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    /help/help/html/features/importvcf.html
JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time

Merge branch 'develop' of http://source.jalview.org/git/jalview into develop

JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April

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    /help/help/html/features/seqfeaturereport.html
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    /help/help/html/features/seqfeaturesrep.png
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    /help/help/html/features/splitView.html
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    /help/help/html/menus/popupMenu.html
JAL-3210 try adding setup method to unit test failing on server...

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    /test/jalview/gui/SeqCanvasTest.java
JAL-1889 corrected wait for consensus to be calculated

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    /test/jalview/gui/AlignFrameTest.java
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    /test/jalview/gui/AlignViewportTest.java
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    /test/jalview/gui/AlignmentPanelTest.java
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    /test/jalview/schemes/PIDColourSchemeTest.java
JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list

Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop