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JAL-4019 Clarification of position on 'X' in help text

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    ./colourSchemes/nucleotideambiguity.html
JAL-4019 small colour fix for X in the documentation

JAL-4019 attribution to Suzanne

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    ./colourSchemes/nucleotideambiguity.html
JAL-4019 Help pages for Nucleotide Ambiguity colour scheme

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    ./colourSchemes/nucleotideambiguity.html
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JAL-4014 Changed gecos display names to match labels in help

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JAL-4065 update citations for Pfam and Rfam and added the Interpro citation

JAL-518 refactored groovy script into main codebase as an Edit Command and alignment view controller method. Left and Right Justify operations now in Edit menu on alignment window and selection popup.

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JAL-4062 copy highlighted region docs, new Alignment window Edit menu option and Shift+Ctrl/CMD-C keystroke

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JAL-4061 JAL-4062 documentation and button labels.. will need revising !

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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

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    ./features/uniprotsequencefetcher.html
JAL-4036 updated help about new UniProt API

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    ./features/uniprotqueryfields.html
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    ./features/uniprotsequencefetcher.html
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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    ./features/uniprotsequencefetcher.html
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JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

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

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JAL-4026 more pointless sleeps

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Merge branch 'develop' into issues/JAL-3553+JAL-3978+JAL-3989+JAL-4014_merged_with_develop

Took Issues Resolved (1 issue) from releases.html 2.11.2.3 row and put

in help/markdown/releases/release-2_11_2_3.md

and regenerated releases.html with

gradle releasesTemplates

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JAL-4014 4 gecos colour schemes added to help documentation

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    ./colourSchemes/gecos-blossom.html
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    ./colourSchemes/gecos-flower.html
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    ./colourSchemes/gecos-ocean.html
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    ./colourSchemes/gecos-sunset.html
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JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3

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JAL-4004 cosmetic improvements for Java documentation renderer

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JAL-4004 working templates and generated whatsNew.html and releases.html file for both browser and Doc viewer

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