jalview

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Commits this week: 97
Total Committers: 68
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Commits this week: 97

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Today
3 hrs ago

Jim Procter

I don't really know what you've commented on here Bob! the 'defect' is an indication that this comment needs to be addressed (somehow) by the recipient of your review. I think you might be talking...

I don't really know what you've commented on here Bob! the 'defect' is an indication that this comment needs to be addressed (somehow) by the recipient of your review.

I think you might be talking about the argsParser here... which is uniquely Jalview-esque, and really designed for Jalview's use as a command line tool. The basic reason for separating the Javascript 'main' and Java 'main' is exactly for this reason - to allow us to exclude functionality not relevant for Javascript use of Jalview.

4 hrs ago

Bob Hanson

Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

Options
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    /src/jalview/structure/StructureSelectionManager.java
4 hrs ago

Bob Hanson

Refactoring of Jalview, JalviewAppLoader, JalviewApp, various applet-related interfaces

- makes JalviewJSApp the JavaScript interface "app" class

- removes JS interface from Jalview

- removes JalviewAppLoader and associated duplication of classes

- adds JavaScript selection and "oninit" listeners (untested)

Options
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    /src/jalview/api/JalviewApp.java
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    /src/jalview/api/JalviewJSApp.java
    • -0
    • +271
    /src/jalview/appletgui/js/JSFunctionExec.java
    • -0
    • +603
    /src/jalview/appletgui/js/JalviewLiteJsApi.java
    • -0
    • +29
    /src/jalview/appletgui/js/JsCallBack.java
    • -0
    • +142
    /src/jalview/appletgui/js/JsSelectionSender.java
    • -0
    • +107
    /src/jalview/appletgui/js/MouseOverListener.java
    • -0
    • +316
    /src/jalview/appletgui/js/MouseOverStructureListener.java
    • -262
    • +287
    /src/jalview/bin/AppletParams.java
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    • +22
    /src/jalview/bin/ArgsParser.java
    • -910
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    /src/jalview/bin/Jalview.java
    • -1500
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    /src/jalview/bin/JalviewAppLoader.java
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    /src/jalview/bin/JalviewJS2.java
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    /src/jalview/bin/JalviewJSApi.java
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    /src/jalview/bin/JalviewLite.java
  16. … 15 more files in changeset.
4 hrs ago

Bob Hanson

SwingJS upgrade for JSUtil and JSUtilI

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    /swingjs/SwingJS-site.zip
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    /swingjs/timestamp
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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/timestamp
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    • +1
    /swingjs/ver/3.2.9/timestamp
4 hrs ago

Bob Hanson

JAL-3446 new Jmol 15.1.3 jar

- into j8lib

- removes netscape package dependence

Options
    • binary
    /j8lib/Jmol-15.1.3.jar
8 hrs ago

Bob Hanson

Let's say we have a number of unknown arguments. Then, I believe, for every two unknown arguments, this code will write (over?) the alignment file that was just loaded. And then, if there is still ...

Let's say we have a number of unknown arguments. Then, I believe, for every two unknown arguments, this code will write (over?) the alignment file that was just loaded. And then, if there is still one more argument left, it will notify us of that one last argument. Am I reading that correctly? I'm going to make this Java-only and instead break if an output format was not identified. I don't know what the plan should be for Java. (I just deleted 30 identical files because I had a pile of unknown parameters.)

[What does "[ ] Defect" mean, below in this form?]

Thursday 04 Jun
8:40 pm

Ben Soares

JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

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    /doc/building.html
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    /doc/building.md
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    /doc/releaseprocess.html
8:40 pm

Ben Soares

JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

Options
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    /doc/building.html
    • -6
    • +6
    /doc/building.md
    • -0
    • +692
    /doc/releaseprocess.html
8:38 pm

Ben Soares

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.

Options
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    /build.gradle
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    /doc/github.css
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    /gradle.properties
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    /utils/doc/github.css
8:38 pm

Ben Soares

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.

Options
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    /build.gradle
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    /doc/github.css
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    /gradle.properties
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    /utils/doc/github.css
5:22 pm

Mungo Carstairs

JAL-1191 reduce logging level for warnings

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    /src/jalview/ext/so/SequenceOntology.java
5:21 pm

Mungo Carstairs

JAL-3446 post-merge unit test fixes, formatting

Options
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    /src/jalview/datamodel/features/FeatureAttributes.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/structure/StructureSelectionManager.java
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    /test/jalview/datamodel/features/FeatureAttributesTest.java
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    /test/jalview/structure/StructureSelectionManagerTest.java
Wednesday 03 Jun
10:30 pm

Bob Hanson

I see...

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    /.gitignore
10:30 pm

Bob Hanson

adds link for __j2sflags.htm to template.html

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    /utils/jalviewjs/site-resources/___j2sflags.htm
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    /utils/jalviewjs/template.html
10:26 pm

Bob Hanson

updated template.html

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    /template.html
10:19 pm

Bob Hanson

_jvjmol.txt

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    /utils/jalviewjs/classlists/_j2sclasslist_jmol.txt
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    /utils/jalviewjs/classlists/_jvjmol.txt
9:54 pm

Bob Hanson

JAL-3664 support for new Locale(""), meaning "not actually a ResourceBundle, just one file (MessageManager)

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    /src/jalview/util/MessageManager.java
9:54 pm

Bob Hanson

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

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    /src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
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    /src/jalview/bin/Cache.java
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    /src/jalview/datamodel/features/FeatureAttributes.java
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    /src/jalview/io/BioJsHTMLOutput.java
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    /src/jalview/urls/IdentifiersUrlProvider.java
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    /swingjs/SwingJS-site.zip
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    /swingjs/timestamp
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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/timestamp
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    /swingjs/ver/3.2.9/SwingJS-site.zip
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    /swingjs/ver/3.2.9/timestamp
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    /utils/jalviewjs/_j2sclasslist.txt
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    /utils/jalviewjs/classlists/_j2sclasslist_jmol.txt
9:47 pm

Bob Hanson

JAL-3446 adds SIFTs JAL-3625 SiftsClient

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    /src/jalview/util/Platform.java
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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
3:24 pm

Bob Hanson

JAL-3446 from JAL-3253 ApplicationSingletonProvider missing for RestClient; others are just cosmetic

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    /src/jalview/datamodel/features/FeatureAttributes.java
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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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    /src/jalview/httpserver/HttpServer.java
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    /src/jalview/io/FileFormats.java
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    /src/jalview/io/cache/AppCache.java
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    /src/jalview/io/gff/SequenceOntologyFactory.java
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    /src/jalview/structure/StructureSelectionManager.java
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    /src/jalview/urls/IdOrgSettings.java
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    /src/jalview/ws/rest/RestClient.java
2:43 pm

Bob Hanson

AsyncSwingWorker setpaused adjustment

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    /src/jalview/gui/SequenceFetcher.java
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    /src/javajs/async/AsyncSwingWorker.java
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    /swingjs/timestamp
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    /swingjs/ver/3.2.9-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/timestamp
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    /swingjs/ver/3.2.9/timestamp
2:12 pm

Bob Hanson

JAL-3446 AsyncSwingWorker upgrade

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    /src/javajs/async/AsyncSwingWorker.java
4:41 am

Bob Hanson

I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

4:05 am

Bob Hanson

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/gui/Desktop.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/jws2/jabaws2/Jws2InstanceFactory.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
1:58 am

Bob Hanson

JAL-3446 from JAL-3253 ApplicationSingletonProvider StructureSelectionManager and others

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    /src/jalview/bin/Jalview.java
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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/FileFormats.java
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    /src/jalview/io/cache/AppCache.java
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    /src/jalview/io/gff/Gff3Helper.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/rest/RestHandler.java
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    /src/jalview/schemes/ColourSchemes.java
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    /src/jalview/structure/StructureImportSettings.java
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    /src/jalview/structure/StructureSelectionManager.java
  16. … 10 more files in changeset.
1:29 am

Bob Hanson

JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop

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    /src/jalview/bin/Jalview.java
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    /src/jalview/datamodel/features/FeatureSources.java
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    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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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/AlignViewport.java
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    /src/jalview/gui/AnnotationLabels.java
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    /src/jalview/gui/AppJmol.java
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    /src/jalview/gui/AssociatePdbFileWithSeq.java
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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/CutAndPasteTransfer.java
  16. … 52 more files in changeset.
12:47 am

Bob Hanson

JAL-3446 from JAL-3253 ApplicationSingletonProvider 1/many

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    /src/jalview/analysis/AlignmentSorter.java
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    /src/jalview/gui/Preferences.java
12:23 am

Bob Hanson

JAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.

- integrated changes from 0b573ed (gmungoc)

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    /test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
Tuesday 02 Jun
11:03 pm

Ben Soares

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.

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    /build.gradle
10:56 pm

Bob Hanson

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

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    /src/jalview/project/Jalview2XML.java