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JAL-4043 what’s new, updated help images and release notes for JAL-4034 (3d beacons button)

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JAL-4036 Added text to help about different number and date range acceptable formats

JAL-4036 updated help about new UniProt API

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
JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new

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

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JAL-3992 fix path

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

JAL-3746 more docs tweaking and release notes

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JAL-3103 updated help doc to remove default browser choice

JAL-3746 structure mapping preference docs for JAL-3817

JAL-3608 JAL-3830 simplified command line docs a bit

JAL-3830 Added new command line usage to docs

JAL-3608 added to LaF documentation

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JAL-3208 release notes and docs for setprop

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JAL-3746 release notes and cli arg docs for JAL-3530

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JAL-3746 release notes JAL-3391 JAL-3829 improved 3dbeacons docs, including documenting ‘best’ and ‘multiple best’ options in 3D-beacons

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JAL-3503 2.11.2.0 release notes and docs

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JAL-3746 JAL-3551 update pymol docs and what’s new text

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JAL-3746 document -no-annotation cli arg

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

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JAL-3551 pymol documentation