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-4028 experiment - THISISAPLACEHOLDER sequences get additional sequence data (as ‘X’) to cover the extent of features on the sequence.

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceDummy.java
JAL-4012 release notes for JAL-1988,JAL-3416

JAL-1988 JAL-3416 avoid unnecessary static flag

JAL-3418 JAL-1988 don’t need java version check anymore

Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

JAL-1988 Hack to ensure Quit dialog box is moved to front

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    /src/jalview/jbgui/APQHandlers.java
JAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop. Use result to not add About and Preferences to normal menus.

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    /src/jalview/jbgui/APQHandlers.java
Merge branch 'develop' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option

JAL-4004 Fix missing whatsNew.html when not building with RELEASE channel set

Merge branch 'improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler' into improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option

Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into improvement/JAL-1988+JAL-3416_flatlaf_osx_apqhandler

JAL-3416 remove flat as default for linux

JAL-1988 JAL-3416 Using the flatlaf-extras About, Preferences and Quit handler system to set APQhandler for both J9+ and now Java 8

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    /src/jalview/gui/APQHandlers.java
JAL-3416 Added some mac specific FlatLAF settings. Note this is not the default macOS LaF, this is only when -Dlaf=flat is set on a mac when running Jalview

JAL-3416 updated FlatLAF libraries to 2.3. Added the flatlaf-extras library

    • binary
    /j11lib/flatlaf-2.3.jar
    • binary
    /j11lib/flatlaf-extras-2.3.jar
    • binary
    /j8lib/flatlaf-2.3.jar
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    /j8lib/flatlaf-extras-2.3.jar
JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

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    /help/help/html/features/pymol.html
Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop

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

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    /help/help/html/releases.html
JAL-4014 release notes for JAL-4026 patches

JAL-4026 increase timeouts for command line ops

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    /test/jalview/bin/CommandLineOperations.java
JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them