jalview

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Commits this week: 4

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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
Friday 24 Jun
5:25 pm

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

JAL-2349 TODO for tests

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    /test/jalview/datamodel/AlignmentTest.java
5:24 pm

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

JAL-2349 JAL-3855 formatting

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    /src/jalview/renderer/ContactMapRenderer.java
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    /src/jalview/ws/dbsources/EBIAlfaFold.java
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    /test/jalview/datamodel/AlignmentTest.java
5:23 pm

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

JAL-4033 TODO re highlighting current column selection

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    /src/jalview/renderer/ContactMapRenderer.java
5:22 pm

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

JAL-2349 debugged and simplified (a little) the scaled rendering of contact maps - still got a rounding error somewhere !

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    /src/jalview/renderer/ContactMapRenderer.java
5:17 pm

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

JAL-3855 update EBI Alphafold barcoded URL generation to v2.cif/json URLs

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    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
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    /src/jalview/ws/dbsources/EBIAlfaFold.java
5:11 pm

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

JAL-2349 JAL-3855 resolve sequence position for contact lookup and catch out bound contact requests

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    /src/jalview/renderer/ContactMapRenderer.java
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    /src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
Friday 10 Jun
12:57 pm

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

JAL-2349 JAL-4027 JAL-3855 quick hack to add contact matrices accompanying alignment objects via sequence fetcher or imported from other sources

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    /src/jalview/gui/AlignViewport.java
12:55 pm

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

JAL-4027 getter for contact matrices on the Alignment.

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentI.java
12:52 pm

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

JAL-1551 formatting

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    /src/jalview/datamodel/Alignment.java
12:13 pm

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

Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

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    /src/jalview/api/AlignViewportI.java
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    /src/jalview/appletgui/AnnotationPanel.java
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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentAnnotation.java
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    /src/jalview/gui/AnnotationPanel.java
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    /src/jalview/io/AppletFormatAdapter.java
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    /src/jalview/renderer/AnnotationRenderer.java
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    /src/jalview/viewmodel/AlignmentViewport.java
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    /src/jalview/ws/SequenceFetcher.java
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    /src/jalview/ws/dbsources/EBIAlfaFold.java
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    /test/jalview/gui/SeqPanelTest.java
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    /test/jalview/ws/seqfetcher/DbRefFetcherTest.java
Thursday 09 Jun
2:25 pm

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

JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

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    /help/help/html/features/pymol.html
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    /help/markdown/releases/release-2_11_2_3.md
2:07 pm

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

Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop

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2:03 pm

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

JAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore

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    /.gitignore
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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
12:35 pm

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

JAL-4014 release notes for JAL-4026 patches

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    /help/markdown/releases/release-2_11_2_3.md
12:16 pm

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

JAL-4026 increase timeouts for command line ops

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    /test/jalview/bin/CommandLineOperations.java
11:20 am

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

JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them

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    /src/jalview/structures/models/AAStructureBindingModel.java
10:38 am

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

JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start.

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    /test/jalview/gui/AlignViewportTest.java
8:18 am

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

JAL-4026 update the viewport’s wrapped width after calculating it

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    /src/jalview/gui/SeqCanvas.java
Wednesday 08 Jun
3:17 pm

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

JAL-4014 release notes for JAL-4023 and JAL-4024

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    /help/markdown/releases/release-2_11_2_3.md
3:11 pm

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

Merge branch 'improvement/JAL-4023_snotation_for_trees' into develop

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3:11 pm

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

Merge branch 'patch/JAL-4024_jumpScrollHang' into develop

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