jalview

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Commits this week: 5
Total Committers: 73
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Commits this week: 5

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Saturday 06 Feb 2021
1:51 am

Ben Soares

JAL-3521 Moved the debian build.gradle to utils/debian/build.gradle.debian

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    • +1361
    /build.gradle
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    • +461
    /utils/debian/build.gradle.debian
Friday 05 Feb 2021
5:25 pm

Jim Procter

Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Release_2_11_1_4_debianpatches

Options
5:24 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_down_build.gradle_for_debian

Options
5:07 pm

Jim Procter

JAL-3814 don’t automatically launch the news browser when the desktop is first opened

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    • -5
    • +8
    /src/jalview/gui/BlogReader.java
5:07 pm

Jim Procter

JAL-3746 JAL-3814 don’t automatically launch the news browser when the desktop is first opened

Options
    • -5
    • +8
    /src/jalview/gui/BlogReader.java
5:07 pm

Jim Procter

JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging www.jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences

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    • -1
    • +6
    /src/jalview/bin/Cache.java
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    • +17
    /src/jalview/gui/Desktop.java
    • -5
    • +0
    /src/jalview/ws/utils/UrlDownloadClient.java
5:07 pm

Jim Procter

JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging www.jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences

Options
    • -1
    • +3
    /src/jalview/bin/Cache.java
    • -17
    • +18
    /src/jalview/gui/Desktop.java
    • -5
    • +0
    /src/jalview/ws/utils/UrlDownloadClient.java
5:05 pm

Jim Procter

JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository

Options
    • -1
    • +5
    /src/jalview/bin/Jalview.java
5:05 pm

Jim Procter

JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository

Options
    • -0
    • +3
    /src/jalview/bin/Cache.java
    • -1
    • +5
    /src/jalview/bin/Jalview.java
5:03 pm

Jim Procter

JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.

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    • -0
    • +2
    /src/jalview/bin/Cache.java
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    /src/jalview/gui/AlignFrame.java
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    • +5
    /src/jalview/gui/Desktop.java
5:03 pm

Jim Procter

JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.

Options
    • -0
    • +2
    /src/jalview/bin/Cache.java
    • -3
    • +29
    /src/jalview/gui/AlignFrame.java
    • -1
    • +25
    /src/jalview/gui/Desktop.java
5:01 pm

Jim Procter

JAL-3746 JAL-3814 NONEWS property

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    • -0
    • +1
    /src/jalview/bin/Cache.java
    • -1
    • +2
    /src/jalview/bin/Jalview.java
5:01 pm

Jim Procter

JAL-3814 NONEWS property

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    • -0
    • +1
    /src/jalview/bin/Cache.java
    • -1
    • +2
    /src/jalview/bin/Jalview.java
2:55 pm

Mateusz Warowny

Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix

Options
2:49 pm

Mateusz Warowny

JAL-3810 - Add trace method to javascript implementation of Logger

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    • -15
    • +25
    /src/jalview/javascript/log4j/Logger.java
2:48 pm

Mateusz Warowny

JAL-3810 - Replace log.trace() calls with log.debug()

Options
    • -2
    • +1
    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
9:20 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2422 updated unit test for ChimeraX command change

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    • -1
    • +1
    /test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
Thursday 04 Feb 2021
5:50 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2422 a fix and a fudge for two failing ChimeraX commands

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    • +1
    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
    • -2
    • +3
    /src/jalview/gui/JalviewChimeraXBindingModel.java
3:09 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3806 fix and test for one-to-many sequence mapping case

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    • -1
    • +0
    /src/jalview/util/MappingUtils.java
    • -20
    • +111
    /test/jalview/util/MappingUtilsTest.java
2:14 pm

Mateusz Warowny

JAL-3809 - Change CompletionStage to CompletableFuture.

Seems that swingjs doesn't have completion stages

properly implemented.

Options
    • -3
    • +3
    /src/jalview/ws/WSClient.java
Wednesday 03 Feb 2021
6:48 pm

Mateusz Warowny

JAL-3809 - fixed param edit for msa but default is broken.

Edit settings dialog now works asynchronously. Everything

works properly in java. In javascript, edit settings dialog

works properly for msa services, but running without the

dialog does not work.

Annotation services do not add annotations to the seuqnces.

Options
    • -39
    • +48
    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/WSClient.java
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    /src/jalview/ws/jws2/MsaWSClient.java
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    • +60
    /src/jalview/ws/jws2/SequenceAnnotationWSClient.java
6:48 pm

Mateusz Warowny

JAL-3809 - Fixed param edit dialog for jalviewjs.

Edit settings dialog now works asynchronously.

Annotation services still do not add annotations to the sequences.

Options
    • -39
    • +48
    /src/jalview/gui/AlignFrame.java
    • -71
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/WSClient.java
    • -36
    • +35
    /src/jalview/ws/jws2/MsaWSClient.java
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    /src/jalview/ws/jws2/SequenceAnnotationWSClient.java
4:34 pm

Jim Procter

JAL-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

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    • -22
    • +138
    /src/jalview/io/gff/ExonerateHelper.java
4:33 pm

Jim Procter

JAL-3808 example exonerate cdna2genome and coding2genome test data and test

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    • +74
    /examples/testdata/test_cdna2genome_showquerygff.gff2
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    /examples/testdata/test_cdna2genome_showtargetgff.gff2
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    /examples/testdata/test_coding2genome_showquerygff.gff2
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    /examples/testdata/test_coding2genome_showtargetgff.gff2
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    • +42
    /test/jalview/io/FeaturesFileTest.java
3:14 pm

Mateusz Warowny

JAL-3878 Initial preparation.

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    • +13
    /src/jalview/util/MathUtils.java
    • -0
    • +67
    /src/jalview/ws2/JalviewWebServiceI.java
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    /src/jalview/ws2/MenuEntryProviderI.java
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    /src/jalview/ws2/MsaMenuEntryProvider.java
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    /src/jalview/ws2/WSJobID.java
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    /src/jalview/ws2/WSJobState.java
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    /src/jalview/ws2/WSJobTrackerI.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
Friday 29 Jan 2021
5:27 pm

Mateusz Warowny

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

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    • +8
    /src/jalview/ws/JPredThread.java
12:35 pm

Mateusz Warowny

This one should be compiling

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    /src/jalview/ws/JPredClient.java
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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/slivkaws/SlivkaWSDiscoverer.java
Thursday 28 Jan 2021
4:56 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3806 more lax allowance (3 positions) for stop codon

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    • -2
    • +2
    /src/jalview/datamodel/AlignedCodonFrame.java
4:56 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3806 (2.11.2 version) more lax allowance (3 positions) for stop codon

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    • -0
    • +137
    /src/jalview/datamodel/AlignedCodonFrame.java
3:39 pm

Mateusz Warowny

Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredClient.java
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    /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/slivkaws/SlivkaJPredServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java