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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-4065 release notes for JAL-4061 JAL-4062

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    ./markdown/releases/release-2_11_2_5.md
JAL-4062 copy highlighted region docs, new Alignment window Edit menu option and Shift+Ctrl/CMD-C keystroke

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    ./help/html/menus/alignmentMenu.html
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JAL-4061 JAL-4062 documentation and button labels.. will need revising !

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JAL-4065 release notes for JAL-4014 and JAL-4063 in 2.11.2.5

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    ./markdown/releases/release-2_11_2_5.md
JAL-4065 - new release notes featuring JAL-3612 fix

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    ./markdown/releases/release-2_11_2_5.md
JAL-4046 release on 9th August 2022

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    ./markdown/releases/release-2_11_2_4.md
JAL-4046 JAL-3993 patch for 2.11.2.4 release

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    ./markdown/releases/release-2_11_2_4.md
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JAL-4046 release notes for JAL-3991

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    ./markdown/releases/release-2_11_2_4.md
JAL-4046 release notes for JAL-4014 - gecos colourschemes

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    ./markdown/releases/release-2_11_2_4.md
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    ./markdown/whatsnew/whatsnew-2_11_2_4.md
JAL-4056 documented in release notes for JAL-4043

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    ./markdown/releases/release-2_11_2_4.md
JAL-4043 what’s new, updated help images and release notes for JAL-4034 (3d beacons button)

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    ./help/html/features/3dbeacons_button.png
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    ./help/html/features/schooser_main.png
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    ./markdown/releases/release-2_11_2_4.md
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    ./markdown/whatsnew/whatsnew-2_11_2_4.md
JAL-4036 Added text to help about different number and date range acceptable formats

JAL-4036 updated help about new UniProt API

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    ./help/html/features/uniprotqueryfields.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-4046 started release notes for 2.11.2.4 patch release

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    ./markdown/releases/release-2_11_2_4.md
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JAL-4012 release date bump and JAL-4004 tweak to include current version in generated whatsNew.html

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    ./markdown/releases/release-2_11_2_3.md
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JAL-4012 updated release date and whats new for 2.11.2.3

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    ./markdown/releases/release-2_11_2_3.md
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    ./markdown/whatsnew/whatsnew-2_11_2_3.md
JAL-4012 tweak release notes wording for legacy.uniprot

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    ./markdown/releases/release-2_11_2_3.md
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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    ./markdown/releases/release-2_11_2_3.md
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    ./markdown/whatsnew/whatsnew-2_11_2_3.md
JAL-4012 release notes for JAL-1988,JAL-3416

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    ./markdown/releases/release-2_11_2_3.md
JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

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