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JAL-3826 Simple configuration with CodeStyle implemented in .editorconfig file

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First commit of 3DB FTS Panel & Restclient

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
Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3822 pass panel height and width to wrapped geometry calculations

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JAL-2422 remove temporary patch (requires ChimeraX Daily or 1.2 build)

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    ./jalview/gui/JalviewChimeraXBindingModel.java
JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    ./jalview/ws/api/JPredServiceI.java
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    ./jalview/ws/jws2/JPredClient.java
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    ./jalview/ws/jws2/JPredThread.java
JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    ./jalview/ws/api/JPredServiceI.java
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    ./jalview/ws/jws2/JPredClient.java
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    ./jalview/ws/jws2/JPredThread.java
JAL-3807 - Move new JPred client to the jws2 package.

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    ./jalview/ws/api/ServiceWithParameters.java
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    ./jalview/ws/jws2/JPredThread.java
JAL-3807 - Move new JPred client to the jws2 package.

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    • +1
    ./jalview/ws/api/ServiceWithParameters.java
    • -0
    • +69
    ./jalview/ws/jws2/JPredClient.java
    • -0
    • +327
    ./jalview/ws/jws2/JPredThread.java
Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

JAL-3807 - Re-implement results processing.

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    ./jalview/ws/JPredThread.java
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    • +5
    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
JAL-3807 - Re-implement results processing.

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    • +114
    ./jalview/ws/JPredThread.java
    • -2
    • +5
    ./jalview/ws/api/JPredMutlipleAlignmentServiceI.java
'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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    ./jalview/ext/jmol/JalviewJmolBinding.java
JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName to set the grouped application name in the taskbar

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

JAL-3814 don’t automatically launch the news browser when the desktop is first opened