jalview

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

Merge branch 'bug/JAL-3809_ws_params_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

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

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    /test/jalview/gui/SeqPanelTest.java
JAL-2422 remove temporary patch (requires ChimeraX Daily or 1.2 build)

JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

Merge branch 'feature/JAL-3692enaEndpoint' into patch/for2.11.2/JAL-3821_ena_rna_moltype

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    /resources/lang/Messages_es.properties
JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna

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/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/48x48/apps/jalview-icon.png
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    /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
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/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/48x48/apps/jalview-icon.png
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    /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
JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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

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

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

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/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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    /src/jalview/ws/JPredThread.java
JAL-3807 - Re-implement results processing.

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    /src/jalview/ws/JPredThread.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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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3818 process Jmol callbacks in AWT thread

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

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    /src/jalview/gui/Desktop.java
JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

JAL-3521 Changed wording of INSTALLATION in source tarball build_properties