jalview

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Commits this week: 21
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Commits this week: 21

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Monday 08 Aug
6:31 pm

Jim Procter

Friday 22 Jul
4:40 pm

Ben Soares

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.

12:34 pm

Jim Procter

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.

12:32 pm

Jim Procter

should be Console.warn

should be Console.warn

12:31 pm

Jim Procter

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).

11:38 am

Jim Procter

shouldn't this be a warn ?

shouldn't this be a warn ?

11:36 am

Jim Procter

this comment block should really be after the imports ?

this comment block should really be after the imports ?

11:35 am

Jim Procter

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 ?

11:33 am

Jim Procter

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
Thursday 16 Jun
12:19 pm

Jim Procter <j.procter@dundee.ac.uk>

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
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    • +37
    /src/jalview/datamodel/features/FeatureStore.java
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    /src/jalview/datamodel/features/SequenceFeatures.java
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    • +7
    /src/jalview/datamodel/features/SequenceFeaturesI.java
Wednesday 15 Jun
4:17 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4012 release notes for JAL-1988,JAL-3416

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    /help/markdown/releases/release-2_11_2_3.md
3:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-1988 JAL-3416 avoid unnecessary static flag

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    /src/jalview/jbgui/APQHandlers.java
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    /src/jalview/jbgui/GDesktop.java
3:54 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /src/jalview/jbgui/GDesktop.java
3:41 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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Monday 13 Jun
6:32 pm

Ben Soares

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

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    • +17
    /src/jalview/jbgui/APQHandlers.java
6:14 pm

Ben Soares

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/gui/APQHandlers.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/jbgui/APQHandlers.java
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    /src/jalview/jbgui/GDesktop.java
5:22 pm

Ben Soares

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

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4:20 pm

Ben Soares

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

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    • +54
    /build.gradle
12:24 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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12:22 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /src/jalview/bin/Jalview.java
11:43 am

Ben Soares

JAL-3416 remove flat as default for linux

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    /src/jalview/bin/Jalview.java
11:20 am

Ben Soares

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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    • +36
    /src/jalview/gui/APQHandlers.java
11:18 am

Ben Soares

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

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    • +28
    /src/jalview/bin/Jalview.java
11:17 am

Ben Soares

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

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    /j11lib/flatlaf-2.1.jar
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    /j11lib/flatlaf-2.3.jar
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    /j11lib/flatlaf-extras-2.3.jar
    • binary
    /j8lib/flatlaf-2.0.1.jar
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    /j8lib/flatlaf-2.3.jar
    • binary
    /j8lib/flatlaf-extras-2.3.jar
Thursday 09 Jun
2:25 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4012 - JAL-4020 release notes and a bit of ‘troubleshooting’ documentation

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    /help/help/html/features/pymol.html
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    /help/markdown/releases/release-2_11_2_3.md
2:07 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'bug/JAL-4020_add_pymolwin_paths' into develop

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2:03 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /.gitignore
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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
12:35 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4014 release notes for JAL-4026 patches

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    /help/markdown/releases/release-2_11_2_3.md
12:16 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 increase timeouts for command line ops

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    • +4
    /test/jalview/bin/CommandLineOperations.java
11:20 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-4026 ignore StructureSelectionManager events if no viewer is available to act on them

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    /src/jalview/structures/models/AAStructureBindingModel.java