jalview

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Commits this week: 4
Total Committers: 73
Last Commit:
Commits this week: 4

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Wednesday 10 Feb 2021
12:12 am

Ben Soares

JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

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    /build.gradle
Monday 08 Feb 2021
7:00 pm

Ben Soares

JAL-3521 Adding a build_properties into sourceDist tarball, with INSTALLATION=SourceDist git-commit...

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    • -0
    • +10
    /build.gradle
7:00 pm

Ben Soares

JAL-3521 Adding a build_properties into sourceDist tarball, with INSTALLATION=SourceDist git-commit...

Options
    • -1
    • +11
    /build.gradle
11:57 am

Ben Soares

JAL-3521 Adjusted wrapper shell script and .desktop file to cater for opening a file with or without -open arg

Options
    • -1
    • +1
    /utils/debian/debian/jalview.desktop
    • -0
    • +17
    /utils/debian/debian/wrappers/jalview
    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl
11:57 am

Ben Soares

JAL-3521 Adjusted wrapper shell script and .desktop file to cater for opening a file with or without -open arg

Options
    • -1
    • +1
    /utils/debian/debian/jalview.desktop
    • -0
    • +17
    /utils/debian/debian/wrappers/jalview
    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl
Sunday 07 Feb 2021
4:06 pm

Jim Procter

JAL-3816 bump version number and cut release notes

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    /RELEASE
    • -220
    • +229
    /doc/building.html
    • -0
    • +30
    /help/help/html/releases.html
4:05 pm

Jim Procter

JAL-3815 default /etc/jalview_properties under utils/debian

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    • +60
    /utils/debian/etc/jalview_properties
4:05 pm

Jim Procter

JAL-3815 default /etc/jalview_properties under utils/debian

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    • +60
    /utils/debian/etc/jalview_properties
Saturday 06 Feb 2021
6:19 pm

Ben Soares

JAL-3251 debian build using maven, simplified build.gradle not needed

Options
    • -461
    • +0
    /utils/debian/build.gradle.debian
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
    • -0
    • +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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    /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
    • -9
    • +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
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    • +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

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    • +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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    • +2
    /src/jalview/bin/Cache.java
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    • +29
    /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
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    • +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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    • +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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    • +1
    /src/jalview/bin/Cache.java
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    • +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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    /src/jalview/javascript/log4j/Logger.java
2:48 pm

Mateusz Warowny

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

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    • +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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    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
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    /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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    /src/jalview/util/MappingUtils.java
    • -20
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    /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.

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    • +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.

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    /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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    /src/jalview/ws/jws2/SequenceAnnotationWSClient.java