jalview

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Commits this week: 8
Total Committers: 73
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Commits this week: 8

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Friday 09 Jul 2021
3:57 pm

Mateusz Warowny

Merge branch 'jpred-fix' into bug/JAL-3807_jpred-with-slivka

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    • -8
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    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
3:44 pm

Mateusz Warowny

JAL-3807 Fix SlivkaWSInstance not fetching alignments.

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    • -1
    • +5
    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Friday 12 Feb 2021
4:19 pm

Mateusz Warowny

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    • -16
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    /src/jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    • +16
    /src/jalview/ws/api/JPredServiceI.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
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    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
11:26 am

Mateusz Warowny

JAL-3807 - Move new JPred client to the jws2 package.

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    • -67
    • +0
    /src/jalview/ws/JPredClient.java
    • -323
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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/api/ServiceWithParameters.java
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    /src/jalview/ws/jws2/JPredClient.java
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    • +327
    /src/jalview/ws/jws2/JPredThread.java
Thursday 11 Feb 2021
4:15 pm

Mateusz Warowny

JAL-3807 - Re-implement results processing.

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    • -13
    • +114
    /src/jalview/ws/JPredThread.java
    • -2
    • +5
    /src/jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
Wednesday 27 Jan 2021
5:11 pm

Mateusz Warowny

JAL-3807 JPred can now successfully submit and track the job.

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    • -0
    • +67
    /src/jalview/ws/JPredClient.java
    • -0
    • +222
    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    /src/jalview/ws/api/ServiceWithParameters.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
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    • +47
    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
2:36 pm

Mateusz Warowny

JAL-3690 Introduce AlignCalcManager2 tests.

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    • -0
    • +7
    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /test/jalview/workers/AlignCaclManager2Test.java
Friday 22 Jan 2021
2:20 pm

Mateusz Warowny

Merge branch 'Jalview-JS/develop' into feature/JAL-3690_callback-based-web-services

Options
Tuesday 19 Jan 2021
5:29 pm

Mateusz Warowny

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    • -87
    • +124
    /src/jalview/workers/AlignCalcManager2.java
4:10 pm

Mateusz Warowny

JAL-3690 AACon ws menu entry fix.

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    • -1
    • +3
    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
Monday 18 Jan 2021
4:50 pm

Mateusz Warowny

JAL-3690 Allow unregistered workers to be run with CalcManager.

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    • -5
    • +10
    /src/jalview/workers/AlignCalcManager2.java
4:50 pm

Mateusz Warowny

JAL-3690 Fix typo in enum name in slivka client.

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    • binary
    /j11lib/slivka-client.jar
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    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
    • binary
    /utils/jalviewjs/libjs/slivka-client-site.zip
12:51 pm

Mateusz Warowny

Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

Options
Friday 15 Jan 2021
6:21 pm

Mateusz Warowny

JAL-3690 Fixed slivka wsmenu categories.

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    • -5
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    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
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    • +1
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Monday 11 Jan 2021
9:30 pm

Ben Soares

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

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    • -4
    • +37
    /build.gradle
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    • +14
    /gradle.properties
9:28 pm

Ben Soares

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/README.txt
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    /swingjs/SwingJS-site.zip
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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
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    /swingjs/ver/3.2.10/differences.txt
  16. … 24 more files in changeset.
Friday 18 Dec 2020
11:37 am

Jim Procter

JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.

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    • -9
    • +15
    /src/jalview/ws/AWSThread.java
Thursday 17 Dec 2020
4:31 pm

Jim Procter

JAL-3690 patch out use of java.streams/spliterator not supported in java2script (yet)

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    • -8
    • +24
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 15 Dec 2020
7:04 pm

Jim Procter

JAL-3690 tweak J2S direct DB access registration for jalview, compbio and other sites

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    • -4
    • +2
    /utils/jalviewjs/coretemplate.html
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    /utils/jalviewjs/template.html
6:46 pm

Jim Procter

JAL-3690 direct access to slivka, compbio, jalview.org and localhost/loopback.

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    • +4
    /utils/jalviewjs/coretemplate.html
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    /utils/jalviewjs/template.html
6:45 pm

Jim Procter

JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

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    /src/jalview/ws/api/JobId.java
6:42 pm

Jim Procter

JAL-3690 patch out spinning animation for web service jobs

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    /src/jalview/gui/WebserviceInfo.java
11:53 am

Jim Procter

JAL-3690 disable proxy server for JalviewJS

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    /utils/jalviewjs/template.html
Monday 14 Dec 2020
7:58 pm

Jim Procter

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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    /src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
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    /src/jalview/analysis/AlignmentSorter.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/AnnotationPanel.java
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    /src/jalview/appletgui/TitledPanel.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/datamodel/Alignment.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/CalculationChooser.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/JvSwingUtils.java
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    /src/jalview/gui/OverviewPanel.java
  16. … 42 more files in changeset.
4:27 pm

Jim Procter

Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

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Friday 11 Dec 2020
2:33 pm

Mateusz Warowny

JAL-3690 Let's enable web services (seriously this time)

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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /swingjs/README.txt
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    /swingjs/SwingJS-site.zip
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    /swingjs/differences.txt
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    /swingjs/net.sf.j2s.core-j11.jar
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    /swingjs/net.sf.j2s.core.jar
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    /swingjs/timestamp
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    /swingjs/ver/3.2.4/DEV_NOTES.txt
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    /swingjs/ver/3.2.4/SwingJS-site.zip
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    /swingjs/ver/3.2.4/_j2sclasslist.txt
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    /swingjs/ver/3.2.4/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.4/timestamp
  16. … 27 more files in changeset.
Thursday 10 Dec 2020
5:50 pm

Jim Procter

JAL-3223 - update swingjs to 3.2.9-j11

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    /swingjs/SwingJS-site.zip
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    /swingjs/differences.txt
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    /swingjs/timestamp
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    /swingjs/ver/3.2.7/SwingJS-site.zip
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    /swingjs/ver/3.2.9-j11/differences.txt
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    /swingjs/ver/3.2.9-j11/net.sf.j2s.core-j11.jar
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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/differences.txt
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    /swingjs/ver/3.2.9/net.sf.j2s.core.jar
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    /swingjs/ver/3.2.9/timestamp
Friday 27 Nov 2020
4:01 pm

Mateusz Warowny

JAL-3690 List.copyOf() workaround

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    • -1
    • +3
    /src/jalview/workers/AlignCalcManager2.java
Friday 13 Nov 2020
3:51 pm

Mateusz Warowny

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/PCAPanel.java
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    /src/jalview/gui/ProgressBar.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/WebserviceInfo.java
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    /src/jalview/workers/AlignCalcManager.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
Thursday 12 Nov 2020
3:13 pm

Mateusz Warowny

JAL-3690 - fixed state inconsistency when restarting the calcworker

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    • -54
    • +22
    /src/jalview/workers/AlignCalcManager2.java