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.
JAL-3980 defensive copy - inefficient but fixes bug

JAL-3981 Additional line breaks - sort of helps

JAL-3981 strategic newlines to help speed up Java's html parser

JAL-3746 bump release date to 10th March - after UoD network maintenance

JAL-3796 include entitlements when codesigning for macOS - doesn't actually help :(

JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

JAL-3746 JAL-3841 fix README typo

JAL-3746 more docs tweaking and release notes

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    /help/help/html/features/preferences.html
Merge branch 'spike/try_spotless_JAL-3438' into develop

JAL-3746 apply copyright to tests

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    /test/jalview/bin/HiDPISettingTest1.java
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JAL-3746 apply copyright to source

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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/ChimeraXManager.java
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    /src/jalview/fts/api/StructureFTSRestClientI.java
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    /src/jalview/fts/service/threedbeacons/.gitignore
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    /src/jalview/gui/ChimeraXViewFrame.java
  1. … 31 more files in changeset.
JAL-3438 spotless for 2.11.2.0

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    /src/com/stevesoft/pat/ChangeRule.java
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    /src/com/stevesoft/pat/Ctrl.java
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    /src/com/stevesoft/pat/FastBracket.java
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    /src/com/stevesoft/pat/Regex.java
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    /src/com/stevesoft/pat/RegexWriter.java
  1. … 647 more files in changeset.
JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

JAL-3108 updated Ensembl client and model species names

JAL-3746 new release date for 2.11.2

JAL-3746 JAL-3103 java.awt.Desktop.showURL method mechanism release notes

Merge branch 'bug/JAL-3103_browser_launcher_problems_macos_and_linux' into develop