jalview

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Commits this week: 6

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Monday 08 Aug
6:31 pm

Jim Procter

Friday 22 Jul
4:40 pm

Ben Soares

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace. This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses...

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace.
This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses. I notice that the new API server is sending back a 400 for bad input (including for non-existent query fields and wrong types for non-string query fields), which is invoking the warning triangle which puts the HTTP error message into the tooltip so this block is now getting more use!

The reason for wanting a full stacktrace in debug mode is that both the API and the changed client are new, so any errors in the next few months will be more quickly diagnosed if we can allow the user to easily obtain a stacktrace of the exception.

12:34 pm

Jim Procter

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a con...

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a convenient [search] button is shown so one doesn't have to click into the query field and press enter to trigger the search again.

12:32 pm

Jim Procter

should be Console.warn

should be Console.warn

12:31 pm

Jim Procter

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalvi...

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalview still work (up until legacy.uniprot.org goes away).

11:38 am

Jim Procter

shouldn't this be a warn ?

shouldn't this be a warn ?

11:36 am

Jim Procter

this comment block should really be after the imports ?

this comment block should really be after the imports ?

11:35 am

Jim Procter

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

11:33 am

Jim Procter

JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
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
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    • +4
    /src/jalview/ws/dbsources/Rfam.java
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    • +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
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    • +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
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    • +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
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    /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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    • +7
    /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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    • +3
    /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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    /test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
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    • +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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    /test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
    • -1
    • +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
    • -1
    • +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
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    /src/jalview/structure/StructureCommandsI.java
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    • +10
    /src/jalview/structures/models/AAStructureBindingModel.java