jalview

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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-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 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

JAL-3521 Updating file opening marker to %u

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    /utils/debian/mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    /utils/debian/debian/jalview-file.png
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    /utils/debian/debian/jalview-icon.png
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    /utils/debian/debian/jalview-mailcap
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    /utils/debian/debian/jalview-mime.xml
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    /utils/debian/debian/jalview.desktop
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    /utils/debian/file_associations_template-mailcap.txt
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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-3521 removed unnecessary parts of the ext project in build.gradle

JAL-3521 Minimal plugins and tasks needed to run tests and build jalview.jar

JAL-3766 what’s new and release notes for 2.11.1.3

JAL-3759 fix compilation error for test

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    /test/jalview/analysis/GroupingTest.java
JAL-3766 release notes for JAL-3759

JAL-3759 exclude hidden columns when processing column selection

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    /src/jalview/analysis/Grouping.java
Merge branch 'documentation/JAL-3766_relnotes' into releases/Release_2_11_1_Branch

Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_11_1_Branch

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3700 mapped sequence group includes short (or all gapped) sequences

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

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    /test/jalview/io/EmblFlatFileTest.java