jalview

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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.

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.

should be Console.warn

should be Console.warn

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).

shouldn't this be a warn ?

shouldn't this be a warn ?

this comment block should really be after the imports ?

this comment block should really be after the imports ?

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 ?

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
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 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
Merge branch 'develop' into improvement/JAL-3594_BG_and_UoD_logos_added

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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    /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
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /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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    /src/jalview/ext/jmol/JmolCommands.java
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    /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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    /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
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    /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