jalview

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JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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    /utils/doc/github.css
JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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    /utils/doc/github.css
JAL-1191 reduce logging level for warnings

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    /src/jalview/ext/so/SequenceOntology.java
JAL-1191 reduce logging level for warnings

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    /src/jalview/ext/so/SequenceOntology.java
JAL-3446 post-merge unit test fixes, formatting

I see...

adds link for __j2sflags.htm to template.html

updated template.html

_jvjmol.txt

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    /utils/jalviewjs/classlists/_jvjmol.txt
JAL-3664 support for new Locale(""), meaning "not actually a ResourceBundle, just one file (MessageManager)

JAL-3664 support for user.home, user.dir, user

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    /src/jalview/urls/IdentifiersUrlProvider.java
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /utils/jalviewjs/classlists/_j2sclasslist_jmol.txt
JAL-3446 adds SIFTs JAL-3625 SiftsClient

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    /src/jalview/ws/sifts/SiftsClient.java
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    /src/jalview/ws/sifts/SiftsSettings.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-3446 from JAL-3253 ApplicationSingletonProvider missing for RestClient; others are just cosmetic

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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/io/gff/SequenceOntologyFactory.java
AsyncSwingWorker setpaused adjustment

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    /src/javajs/async/AsyncSwingWorker.java
    • binary
    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
JAL-3446 AsyncSwingWorker upgrade

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    /src/javajs/async/AsyncSwingWorker.java
JAL-3446 from JAL-3253 Discoverers

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/urls/IdOrgSettings.java
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    /src/jalview/ws/jws1/Discoverer.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
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    /src/jalview/ws/rest/RestClient.java
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    /src/jalview/ws/sifts/SiftsSettings.java
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    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-3446 from JAL-3253 ApplicationSingletonProvider StructureSelectionManager and others

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    /src/jalview/ext/ensembl/EnsemblCds.java
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    /src/jalview/ext/ensembl/EnsemblGene.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/io/cache/AppCache.java
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    /src/jalview/io/gff/InterProScanHelper.java
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    /src/jalview/io/gff/SequenceOntologyFactory.java
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    /src/jalview/schemes/ColourSchemes.java
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    /src/jalview/structure/StructureImportSettings.java
  1. … 10 more files in changeset.
JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop

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    /src/jalview/gui/AlignExportOptions.java
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    /src/jalview/gui/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/ChimeraViewFrame.java
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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/CutAndPasteTransfer.java
  1. … 52 more files in changeset.
JAL-3446 from JAL-3253 ApplicationSingletonProvider 1/many

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    /src/jalview/analysis/scoremodels/ScoreModels.java
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    /src/jalview/bin/ApplicationSingletonProvider.java
JAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.

- integrated changes from 0b573ed (gmungoc)

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/SeqCanvas.java
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    /test/jalview/gui/SeqCanvasTest.java
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    /test/jalview/ws/PDBSequenceFetcherTest.java
JAL-3225 Using Gradle Git-Version plugin to set gitHash and gitBranch

Using Gradle Git-Version instead of exec to run git directly allows

buildship to successfully import the project into eclipse without a

command line git installed. Essential for development within Eclipse in

Windows without having to install either gradle or git as command line

tools.

JAL-3446 from JAL-3253-applet Jalview2XML integration (retains GeneLocus; switches to invokeLater)

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    /src/jalview/project/Jalview2XML.java
JAL-3446 from JAL-3253-applet Desktop and Jws2Discoverer getInstance()

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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-3446 JAL-3401 from JAL-3253-applet AlignmentPanel.holdRepaint

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    /src/jalview/gui/AlignmentPanel.java
preferences/StructureViewer fix

preferences/StructureViewer fix

JAL-3446 from JAL-3253 AppletFormatAdapter not fixed

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    /src/jalview/io/AppletFormatAdapter.java
Preferences/StructureViewer fix

JAL-3446 I don't understand how this bug could be here.

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    /src/jalview/io/AppletFormatAdapter.java
JAL-3445 JAL-3253 BSML bbb format test data - pox virus genomes

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    /examples/testdata/10-poxgenomes.bbb