jalview

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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).

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
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-3117 raise AlignFrame or SplitFrame when Overview clicked

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/gui/ViewSelectionMenu.java
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    /src/jalview/jbgui/GAlignFrame.java
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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3117 bring alignment to foreground on click on Overview

Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

JAL-3594 Better Jalview Develop banner

JAL-3594 Documentation added to building.md for using the utils/channels/... folders

Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into develop

JAL-3594 Improved About banners for develop and test-release

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    /utils/channels/develop/images/jalview_develop_banner.xcf
JAL-3594 Images for splash screen

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    /resources/default_images/UoD_banner-28.png
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    /resources/default_images/UoD_banner-32.png
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    /resources/default_images/UoD_banner.png
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    /resources/default_images/barton_group-28.png
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    /src/jalview/util/ChannelProperties.java
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JAL-3594 JAL-3728 Added taskbar icons to desktop and Java console. Changed "Jalview" to "app_name" in various appropriate places

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    /src/jalview/util/ChannelProperties.java
Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into merge/JAL-3594_and_new_develop_issues

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    /src/jalview/bin/Jalview.java
JAL-3594 Change main window title

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    /utils/install4j/README-DMG_creation.md
JAL-3594 DMG fixes

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    /utils/install4j/README-DMG_background_image_creation.md
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    /utils/install4j/README-DMG_creation.md
JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

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    /src/jalview/util/ChannelProperties.java
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    /utils/channels/default/channel_gradle.properties
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    /utils/channels/default/images/barton_group-white.svg
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    /utils/channels/default/images/barton_group.svg
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    /utils/channels/default/images/jalview_default_dmg_DS_Store
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JAL-3754 Fixed jar task creating strange dir because of outputs.file()