jalview

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Wednesday 30 Jun 2021
1:32 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

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    • -0
    • +7
    /build.gradle
11:31 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3842 JAL-3746 (need to cherry pick to develop) - automatically generate link to latest release notes in what's new

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    /help/help/html/whatsNew.html
Wednesday 09 Jun 2021
6:06 pm

Jim Procter

JAL-3842 2.11.1.5 what’s new, release notes, and version bump

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    /RELEASE
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    • +70
    /help/help/html/releases.html
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    • +5
    /help/help/html/whatsNew.html
5:38 pm

Jim Procter

Merge branch 'patch/JAL-3840_2_11_1_4' into releases/Release_2_11_1_Branch

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4:53 pm

Jim Procter

JAL-3840 don’t update the modal residue count for gaps

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    • +6
    /src/jalview/datamodel/ResidueCount.java
4:40 pm

Jim Procter

fixes JAL-3840

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    /src/jalview/datamodel/ResidueCount.java
4:35 pm

Jim Procter

JAL-3840 failing test - show that addGaps overflows

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    /src/jalview/datamodel/ResidueCount.java
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    /test/jalview/datamodel/ResidueCountTest.java
Monday 26 Apr 2021
6:27 pm

Ben Soares

JAL-3248 Archived old README. Added new README to point user to doc/building.md

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    /README
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    /doc/old_ant_build_README
5:56 pm

Ben Soares

JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

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    /build.gradle
Monday 19 Apr 2021
4:37 pm

Ben Soares

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

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    /src/jalview/bin/HiDPISetting.java
Tuesday 09 Mar 2021
1:03 pm

Jim Procter

JAL-3816 release date updated to 9th March

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    /help/help/html/releases.html
Friday 05 Mar 2021
6:19 pm

Jim Procter

JAL-3816 release date set for 8th March and updated what's new

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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
5:44 pm

Jim Procter

JAL-3816 new known defects JAL-3705 and JAL-3806

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    • +15
    /help/help/html/releases.html
Thursday 04 Mar 2021
11:44 am

Jim Procter

Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"

This reverts commit cb628aab46f9027e71b71203b322f96710e09990, reversing

changes made to a40669b2eeb34a6c760b63c172a31a194b456f24.

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    /src/jalview/datamodel/AlignedCodonFrame.java
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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
11:39 am

Jim Procter

Revert "JAL-3816 release notes for JAL-3806"

This reverts commit ead40d75a04715c80c61e34e277bb995cb2bef90.

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    /help/help/html/releases.html
Friday 26 Feb 2021
3:02 pm

Jim Procter

JAL-3816 release notes for JAL-3806

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    • +1
    /help/help/html/releases.html
2:02 pm

Jim Procter

Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch

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1:55 pm

Jim Procter

JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818 release notes and date for 2.11.1.4 release

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    /help/help/html/releases.html
Wednesday 24 Feb 2021
4:49 pm

Jim Procter

Merge branch 'bug/JAL-3818_jmolDeadlock' into releases/Release_2_11_1_Branch

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4:48 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch

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Friday 12 Feb 2021
6:24 pm

Ben Soares

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/16x16/mimetypes/x-jalview-file.png
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    /utils/debian/debian/icons/22x22/mimetypes/x-jalview-file.png
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    /utils/debian/debian/icons/24x24/mimetypes/x-jalview-file.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/32x32/mimetypes/x-jalview-file.png
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    /utils/debian/debian/icons/48x48/apps/jalview-icon.png
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    /utils/debian/debian/icons/48x48/mimetypes/x-jalview-file.png
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    /utils/debian/debian/icons/512x512/apps/jalview-icon.png
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    /utils/debian/debian/icons/512x512/mimetypes/x-jalview-file.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
Thursday 11 Feb 2021
11:30 am

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

JAL-3818 process Jmol callbacks in AWT thread

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    • +47
    /src/jalview/ext/jmol/JalviewJmolBinding.java
Wednesday 10 Feb 2021
12:19 am

Ben Soares

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

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    /src/jalview/gui/Desktop.java
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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    /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

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    /utils/debian/debian/jalview.desktop
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    /utils/debian/debian/wrappers/jalview
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    /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
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    /doc/building.html
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    /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
Saturday 06 Feb 2021
6:19 pm

Ben Soares

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

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    /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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    /build.gradle
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    /utils/debian/build.gradle.debian