jalview

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make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
Looks good. I've bumped the version to 1.8.3-1.2.12 and recompiled jars.

Looks good. I've bumped the version to 1.8.3-1.2.12 and recompiled jars.

JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
JAL-3417 groovy script enables per group consensus and sequence logos for all so the sdppred calculation actually has something to work on

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    /examples/groovy/sdppred_testing.groovy
JAL-3417 propagate description from AnnotationProvider to the worker

Merge branch 'features/JAL-3417_sdppred_calcs' into features/r2_11_2_JAL-3417_sdppred

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/SequenceGroup.java
JAL-3551 patch superpose test for additional undo dis/enable commands

JAL-3959 add key retrieval urls that support CORS needed by JalviewJS

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    /src/jalview/ws/ebi/EBIFetchClient.java
JAL-3746 more release notes and docs: JAL-3863 JAL-3745

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    /help/help/html/features/structurechooser.html
JAL-3746 release notes.. in progress

JAL-3551 - wrap pair_fit with undo_disable and undo_enable

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3837 GPL license on splashscreen (finally !) and added link to discourse.jalview.org to replace mailing list

JAL-3949 report Pymol XMLRPC port via log.info

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    /src/jalview/ext/pymol/PymolManager.java
JAL-1761 backbone type parameter for configuring which atoms are used for superposition of structures

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-1761 need to pass molecule type when generating superposition commands

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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3551 patch test for altloc handling atom spec in superposition code

JAL-1761 need to pass molecule type when generating superposition commands

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3906 use indicate to highlight current mousedOver residue in Jalview in a Pymol view

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    /src/jalview/gui/PymolBindingModel.java
JAL-3746 update release date to later in Feb 2022

JAL-3551 pymol documentation

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    /help/help/html/features/pymol.html
Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authoritative_IDs' into develop

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overriding any embedded IDs

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    /src/jalview/datamodel/PDBEntry.java
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    /test/jalview/datamodel/PDBEntryTest.java
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop

Conflicts:

test/jalview/bin/CommandLineOperations.java

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    /test/jalview/bin/CommandLineOperations.java
JAL-3949 fix testProps path and make line count more accurate

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    /test/jalview/bin/CommandLineOperations.java
JAL-3949 increase command line ops test timeout

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    /test/jalview/bin/CommandLineOperations.java