jalview

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Commits this week: 7
Total Committers: 71
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Commits this week: 7

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Friday 26 Feb
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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    • -3
    • +3
    /help/help/html/releases.html
Thursday 25 Feb
3:57 pm

Mungo Carstairs

3:56 pm

Mungo Carstairs

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

2:21 pm

Mungo Carstairs

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

2:17 pm

Mungo Carstairs

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

2:14 pm

Mungo Carstairs

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

Wednesday 24 Feb
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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4:45 pm

Jim Procter

4:43 pm

Jim Procter

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
Friday 12 Feb
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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    • binary
    /utils/debian/debian/icons/128x128/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/16x16/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/16x16/mimetypes/x-jalview-file.png
    • binary
    /utils/debian/debian/icons/22x22/mimetypes/x-jalview-file.png
    • binary
    /utils/debian/debian/icons/24x24/mimetypes/x-jalview-file.png
    • binary
    /utils/debian/debian/icons/256x256/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/32x32/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/32x32/mimetypes/x-jalview-file.png
    • binary
    /utils/debian/debian/icons/48x48/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/48x48/mimetypes/x-jalview-file.png
    • binary
    /utils/debian/debian/icons/512x512/apps/jalview-icon.png
    • binary
    /utils/debian/debian/icons/512x512/mimetypes/x-jalview-file.png
    • binary
    /utils/debian/debian/icons/64x64/apps/jalview-icon.png
    • binary
    /utils/debian/debian/jalview-file.png
    • -22
    • +22
    /utils/debian/debian/jalview-mime.xml
    • -1
    • +1
    /utils/debian/file_associations_template-shared-mime-info.xml
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    • +1
    /utils/debian/mime_types_for_debian.pl
Thursday 11 Feb
5:06 pm

Mungo Carstairs

Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

3:00 pm

Mungo Carstairs

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly). Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatibl...

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly).
Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatible syntax).

2:27 pm

Mungo Carstairs

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

2:26 pm

Mungo Carstairs

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

2:17 pm

Mungo Carstairs

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

12:29 pm

Mungo Carstairs

JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3809: Edit web service parameters dialog does not work in jalviewjs
11:30 am

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

JAL-3818 process Jmol callbacks in AWT thread

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    • -23
    • +47
    /src/jalview/ext/jmol/JalviewJmolBinding.java
Wednesday 10 Feb
12:19 am

Ben Soares

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

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    • -44
    • +65
    /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
7:00 pm

Ben Soares

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

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    • +10
    /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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    • +1
    /utils/debian/debian/jalview.desktop
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    • +17
    /utils/debian/debian/wrappers/jalview
    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl
Sunday 07 Feb
4:06 pm

Jim Procter

JAL-3816 bump version number and cut release notes

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    • -1
    • +1
    /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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    • -0
    • +60
    /utils/debian/etc/jalview_properties
Saturday 06 Feb
6:19 pm

Ben Soares

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

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    • -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
5:25 pm

Jim Procter

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

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5:24 pm

Jim Procter

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

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