jalview

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Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4046 release on 9th August 2022

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4046 JAL-3993 imports reformatting

JAL-4046 JAL-3993 patch for 2.11.2.4 release

JAL-4046 release notes for JAL-3991

Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop

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    /resources/lang/Messages_es.properties
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4046 release notes for JAL-4014 - gecos colourschemes

Merge branch 'improvement/JAL-4014_gecos_colour_schemes' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-4056 documented in release notes for JAL-4043

Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

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

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    /help/help/html/features/3dbeacons_button.png
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    /help/help/html/features/schooser_main.png
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    /help/markdown/whatsnew/whatsnew-2_11_2_4.md
JAL-4034 show the loading spinner when switching between tabs

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    /src/jalview/gui/StructureChooser.java
Merge branch 'features/JAL-4034_improve_3dbeacons_button_and_ux' into develop

JAL-4056 fixed tl;dr section of doc/building.md

JAL-4055 quick patch to see how Jalview looks as a free-floating multiwindowed app rather than a Desktop contained app

JAL-4048 feature group filter

JAL-4036 Fixed the virus_host_id query field

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    /resources/fts/uniprot_data_columns-2022.txt
JAL-4036 Added text to help about different number and date range acceptable formats

JAL-4036 updated help about new UniProt API

JAL-4036 moved a comment block

JAL-4034 button looks better also on other OSes with the 0 vertical insets

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    /src/jalview/jbgui/GStructureChooser.java
JAL-4034 add round corners to 3DB confirmation button with icon on a mac

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    /src/jalview/jbgui/GStructureChooser.java
JAL-4036 Changes made from code review CR-JAL-265

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.

JAL-4048 fix disappearing sequence IDs, and non-positional feature descriptions