jalview

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

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

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.

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).

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

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).

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

Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
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
    • 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/48x48/apps/jalview-icon.png
    • binary
    /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
Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

'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).

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.

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.

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.

JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3818 process Jmol callbacks in AWT thread

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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