jalview

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Commits this week: 2
Total Committers: 73
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Commits this week: 2

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Wednesday 30 Mar
4:23 pm

Jim Procter

4:22 pm

Jim Procter

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...
4:20 pm

Jim Procter

JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
Monday 07 Mar
8:03 pm

Jim Procter

Thursday 03 Mar
9:26 am

Ben Soares

9:26 am

Ben Soares

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.

Wednesday 02 Mar
12:20 pm

Jim Procter

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
Wednesday 23 Feb
2:27 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3417 groovy script enables per group consensus and sequence logos for all so the sdppred calculation actually has something to work on

Options
    • -2
    • +7
    /examples/groovy/sdppred_testing.groovy
2:26 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3417 propagate description from AnnotationProvider to the worker

Options
    • -0
    • +3
    /src/jalview/workers/AnnotationWorker.java
12:47 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
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    • +58
    /src/jalview/datamodel/Alignment.java
    • -0
    • +22
    /src/jalview/datamodel/SequenceGroup.java
    • -0
    • +4
    /src/jalview/viewmodel/AlignmentViewport.java
Thursday 17 Feb
5:15 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 patch superpose test for additional undo dis/enable commands

Options
    • -3
    • +3
    /test/jalview/ext/pymol/PymolCommandsTest.java
3:05 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
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    • +4
    /src/jalview/bin/Jalview.java
    • -0
    • +4
    /src/jalview/ws/dbsources/Pfam.java
    • -0
    • +4
    /src/jalview/ws/dbsources/Rfam.java
    • -1
    • +3
    /src/jalview/ws/ebi/EBIFetchClient.java
12:58 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 more release notes and docs: JAL-3863 JAL-3745

Options
    • -1
    • +1
    /help/help/html/features/chimera.html
    • -2
    • +2
    /help/help/html/features/pymol.html
    • -19
    • +17
    /help/help/html/features/structurechooser.html
    • -2
    • +6
    /help/help/html/releases.html
    • -18
    • +54
    /help/help/html/whatsNew.html
Wednesday 16 Feb
6:43 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 release notes.. in progress

Options
    • -3
    • +15
    /help/help/html/releases.html
6:43 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 - wrap pair_fit with undo_disable and undo_enable

Options
    • -1
    • +4
    /src/jalview/ext/pymol/PymolCommands.java
4:34 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3837 GPL license on splashscreen (finally !) and added link to discourse.jalview.org to replace mailing list

Options
    • -11
    • +19
    /src/jalview/gui/Desktop.java
    • -1
    • +1
    /src/jalview/gui/SplashScreen.java
3:51 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3949 report Pymol XMLRPC port via log.info

Options
    • -1
    • +1
    /src/jalview/ext/pymol/PymolManager.java
Tuesday 15 Feb
5:35 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-1761 backbone type parameter for configuring which atoms are used for superposition of structures

Options
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    /src/jalview/ext/jmol/JmolCommands.java
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    • +13
    /src/jalview/ext/pymol/PymolCommands.java
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    • +16
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    • +13
    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
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    /src/jalview/structure/StructureCommandsBase.java
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    • +5
    /src/jalview/structure/StructureCommandsI.java
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    /src/jalview/structures/models/AAStructureBindingModel.java
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    • +13
    /test/jalview/ext/jmol/JmolCommandsTest.java
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    /test/jalview/ext/pymol/PymolCommandsTest.java
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    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
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    • +25
    /test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
    • -5
    • +6
    /test/jalview/structures/models/AAStructureBindingModelTest.java
4:55 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
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    • +1
    /test/jalview/ext/jmol/JmolCommandsTest.java
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    • +1
    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
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    • +1
    /test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
4:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 patch test for altloc handling atom spec in superposition code

Options
    • -5
    • +5
    /test/jalview/ext/pymol/PymolCommandsTest.java
4:47 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
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    • +1
    /src/jalview/ext/jmol/JmolCommands.java
    • -1
    • +1
    /src/jalview/ext/pymol/PymolCommands.java
    • -1
    • +1
    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
    • -1
    • +1
    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
    • -1
    • +3
    /src/jalview/structure/StructureCommandsI.java
    • -3
    • +10
    /src/jalview/structures/models/AAStructureBindingModel.java
4:46 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3906 use indicate to highlight current mousedOver residue in Jalview in a Pymol view

Options
    • -13
    • +3
    /src/jalview/gui/PymolBindingModel.java
4:45 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 update release date to later in Feb 2022

Options
    • -1
    • +1
    /help/help/html/releases.html
4:44 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551 pymol documentation

Options
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    • +62
    /help/help/html/features/pymol.html
Monday 14 Feb
11:02 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authoritative_IDs' into develop

Options
10:58 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3551

Options
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    • +5
    /src/jalview/ext/pymol/PymolCommands.java
2:03 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overriding any embedded IDs

Options
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    • +28
    /src/jalview/datamodel/PDBEntry.java
    • -0
    • +1
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
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    • +16
    /test/jalview/datamodel/PDBEntryTest.java
Saturday 12 Feb
11:49 am

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop

Conflicts:

test/jalview/bin/CommandLineOperations.java

Options
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    • +3
    /test/jalview/bin/CommandLineOperations.java
10:09 am

Ben Soares

JAL-3949 fix testProps path and make line count more accurate

Options
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    • +3
    /test/jalview/bin/CommandLineOperations.java
    • -0
    • +1
    /test/jalview/bin/testProps.jvprops
Friday 11 Feb
6:52 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3949 increase command line ops test timeout

Options
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    • +1
    /test/jalview/bin/CommandLineOperations.java