jalview

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JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

Merge branch 'feature/JAL-3692enaEndpoint' into patch/for2.11.2/JAL-3821_ena_rna_moltype

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    /resources/lang/Messages_es.properties
JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna

JAL-3521 High quality file icons for jalview associated files, and associated mime-type icon references

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    /utils/debian/debian/icons/128x128/apps/jalview-icon.png
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    /utils/debian/debian/icons/16x16/apps/jalview-icon.png
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    /utils/debian/debian/icons/256x256/apps/jalview-icon.png
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    /utils/debian/debian/icons/32x32/apps/jalview-icon.png
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    /utils/debian/debian/icons/48x48/apps/jalview-icon.png
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    /utils/debian/debian/icons/512x512/apps/jalview-icon.png
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    /utils/debian/debian/icons/64x64/apps/jalview-icon.png
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    /utils/debian/debian/jalview-file.png
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    /utils/debian/debian/jalview-mime.xml
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    /utils/debian/file_associations_template-shared-mime-info.xml
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    /utils/debian/mime_types_for_debian.pl
JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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

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    /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
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 - 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

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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