jalview

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Commits this week: 21
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Commits this week: 21

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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
Monday 06 Jun
2:09 pm

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

JAL-4023 use %g for distances (scientific notation for very small or large values)

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    /src/jalview/gui/TreeCanvas.java
12:22 pm

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

JAL-4023 store distances as doubles

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    /src/jalview/datamodel/SequenceNode.java
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    /src/jalview/io/NewickFile.java
Wednesday 11 May
3:50 pm

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

Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3

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1:44 pm

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

JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3

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    /RELEASE
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    /help/help/html/releases.html
Tuesday 10 May
5:56 pm

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

JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !

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    /THIRDPARTYLIBS
    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
Tuesday 19 Apr
3:04 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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3:03 pm

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

JAL-3992 bump version and report updates in 2.11.2.2 release notes

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    /RELEASE
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    /help/help/html/releases.html
3:02 pm

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

Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop

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2:57 pm

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

Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop

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Monday 18 Apr
2:49 pm

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

JAL-3997 check for tooltip being null before checking equivalence to last tooltip string

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    /src/jalview/gui/SeqPanel.java
1:27 pm

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

Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

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12:51 pm

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

JAL-3992 fix path

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    /help/help/html/features/cursorMode.html
Saturday 16 Apr
1:36 pm

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

JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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    /src/jalview/datamodel/AlignmentAnnotation.java
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    /src/jalview/io/StockholmFile.java
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    /test/jalview/io/StockholmFileTest.java
Wednesday 13 Apr
4:13 pm

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

JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode

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    /help/help/html/features/cursorMode.html
Tuesday 05 Apr
8:48 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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8:44 pm

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

JAL-3990 release notes and what’s new

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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
6:50 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:37 pm

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

JAL-3981 patch tests and remove errant imports

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    /src/jalview/io/SequenceAnnotationReport.java
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    /test/jalview/io/SequenceAnnotationReportTest.java
6:15 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:14 pm

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

JAL-3990 gradle spotlessApply

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    /src/jalview/gui/structurechooser/TDBResultAnalyser.java
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    /src/jalview/io/SequenceAnnotationReport.java
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    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
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    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
6:12 pm

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

JAL-3990 release notes for 2.11.2.1 patch release

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    /help/help/html/releases.html