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
JAL-3288 Replace all javax.swing.JInternalFrame with extended jalview.jbgui.ClassicJInternalFrame

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    /src/jalview/gui/AnnotationChooser.java
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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationExporter.java
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    /src/jalview/gui/AnnotationRowFilter.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/ChimeraViewFrame.java
  1. … 26 more files in changeset.
JAL-3991 Made info displayed only when needed (Java 11+)

JAL-3991 Added information output about the slightly alarming 'WARNING: An illegal reflective access operation has occurred' error that occurs for linux users. It can't be avoided so informing the user should help with alarm levels.

JAL-3991 JAVA_COMPILE_VERSION put into build_properties. Check for possible JVM mismatch in jalview.bin.LaunchUtils. STDERR warning from jalview.bin.Launcher. Console and optional popup warning in jalview.bin.Jalview.

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    /resources/lang/Messages_es.properties
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    /src/jalview/util/LaunchUtils.java
JAL-3981 patch tests and remove errant imports

JAL-3990 gradle spotlessApply

JAL-3990 release notes for 2.11.2.1 patch release

Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop

JAL-3983 release note for JAL-3985

Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop

JAL-3085 update tests and mock responses, new P0dtd1 testcase

JAL-3985 formatting

JAL-3985 split PDB id queries into multiple queries so server doesn’t 414

Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop

JAL-3976 fix mock PDBFTS query & responses

JAL-3983 known issue note for JAL-3984

JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984

Merge branch 'bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog' into develop

JAL-360 JAL-3975 update parent for text colour dialog - doesn't seem to help but we live in hope..

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    /src/jalview/gui/TextColourChooser.java
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...