jalview

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

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Re-implement results processing.

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    /src/jalview/ws/JPredThread.java
JAL-3807 - Re-implement results processing.

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    /src/jalview/ws/JPredThread.java
JAL-3818 process Jmol callbacks in AWT thread

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName to set the grouped application name in the taskbar

JAL-3521 Change grouped Jalview windows on linux taskbar to have name Jalview

JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

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

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

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

    • -0
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    /utils/debian/debian/wrappers/jalview
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    /utils/debian/mime_types_for_debian.pl
JAL-3816 bump version number and cut release notes

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

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    /utils/debian/etc/jalview_properties
JAL-3251 debian build using maven, simplified build.gradle not needed

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

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    /utils/debian/build.gradle.debian
Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Release_2_11_1_4_debianpatches

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

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

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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    /src/jalview/ws/utils/UrlDownloadClient.java
JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository

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

JAL-3814 NONEWS property

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

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

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    /src/jalview/javascript/log4j/Logger.java
JAL-3810 - Replace log.trace() calls with log.debug()

JAL-2422 updated unit test for ChimeraX command change

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

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

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    /test/jalview/util/MappingUtilsTest.java
JAL-3809 - Change CompletionStage to CompletableFuture.

Seems that swingjs doesn't have completion stages

properly implemented.

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/jws2/MsaWSClient.java