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 bumped the version to 1.8.3-1.2.12 in source and libraries

    • binary
    /getdown/lib/getdown-launcher-local.jar
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-3691 rebuilt getdown jars

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 getdown - needs rebuild / redacting

JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src

JAL-3746 release notes.. in progress

JAL-3551 - wrap pair_fit with undo_disable and undo_enable

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    • +4
    /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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    • +1
    /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
    • -12
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    • +13
    /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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    • +1
    /src/jalview/ext/jmol/JmolCommands.java
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    • +1
    /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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    • +3
    /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
    • -1
    • +16
    /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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    • +3
    /test/jalview/bin/CommandLineOperations.java
JAL-3949 increase command line ops test timeout

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    • +1
    /test/jalview/bin/CommandLineOperations.java
JAL-3949 ensure Jalview command line ops setup actually quits after SETUP_TIME milliseconds - seems there’s less stderr noise than before !

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    • +43
    /test/jalview/bin/CommandLineOperations.java
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop

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    • +2
    /src/jalview/gui/StructureViewerBase.java