jalview

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Commits this week: 21
Total Committers: 73
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Commits this week: 21

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Monday 08 Aug
6:31 pm

Jim Procter

Monday 25 Jul
10:57 am

Ben Soares

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

Options
    • -7
    • +4
    /src/jalview/jbgui/GStructureChooser.java
Sunday 24 Jul
5:37 pm

Ben Soares

JAL-4034 add round corners to 3DB confirmation button with icon on a mac

Options
    • -4
    • +14
    /src/jalview/jbgui/GStructureChooser.java
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
Friday 15 Jul
6:38 pm

Ben Soares

JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can moveToFront. Minor improvement to Search 3DB button appearance

Options
    • -21
    • +21
    /src/jalview/gui/StructureChooser.java
    • -3
    • +16
    /src/jalview/jbgui/GStructureChooser.java
6:37 pm

Ben Soares

JAL-4034 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (similar to JalviewJS)

Options
    • -14
    • +137
    /src/jalview/gui/JvOptionPane.java
Tuesday 12 Jul
12:13 pm

Ben Soares

JAL-4034 change to jalview property name

Options
    • -1
    • +1
    /src/jalview/gui/StructureChooser.java
11:58 am

Ben Soares

JAL-4034 showConfirmDialog works for both desktop and jalviewjs

Options
    • -17
    • +2
    /src/jalview/gui/StructureChooser.java
Monday 11 Jul
5:14 pm

Ben Soares

JAL-4034 Non-blocking 3D Beacons query after warning dialog

Options
    • -17
    • +36
    /src/jalview/gui/StructureChooser.java
4:25 pm

Ben Soares

JAL-4034 allow a jalview_property to set the threshold level

Options
    • -2
    • +5
    /src/jalview/gui/StructureChooser.java
Monday 04 Jul
6:04 pm

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

JAL-4034 fix #3 change uniprot ref fetch dialog to a ‘warning’ shown when many ids have to be retrieved

Options
    • -1
    • +1
    /resources/lang/Messages.properties
    • -2
    • +10
    /src/jalview/gui/StructureChooser.java
5:59 pm

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

JAL-4034 Fix #2 show an icon and a button to press to initiate search

Options
    • -0
    • +4
    /src/jalview/gui/StructureChooser.java
    • -17
    • +20
    /src/jalview/jbgui/GStructureChooser.java
5:58 pm

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

JAL-4034 fix 1 - reword button

Options
    • -1
    • +1
    /resources/lang/Messages.properties
3:58 pm

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

JAL-4012 updated release date and whats new for 2.11.2.3

Options
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    • +1
    /help/markdown/releases/release-2_11_2_3.md
    • -1
    • +1
    /help/markdown/whatsnew/whatsnew-2_11_2_3.md
Friday 01 Jul
2:08 pm

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

JAL-4012 tweak release notes wording for legacy.uniprot

Options
    • -1
    • +1
    /help/markdown/releases/release-2_11_2_3.md
1:55 pm

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

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

Options
1:44 pm

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

JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new

Options
    • -0
    • +8
    /help/help/html/features/uniprotsequencefetcher.html
    • -0
    • +2
    /help/markdown/releases/release-2_11_2_3.md
    • -1
    • +1
    /help/markdown/whatsnew/whatsnew-2_11_2_3.md
Thursday 30 Jun
5:37 pm

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

JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)

Options
    • -11
    • +16
    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
Tuesday 28 Jun
1:32 pm

Ben Soares

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

Options
    • -1
    • +4
    /src/jalview/jbgui/GDesktop.java
1:31 pm

Ben Soares

JAL-1988 Don't put Quit in the File menu if there's a handler for it

Options
    • -1
    • +4
    /src/jalview/jbgui/GDesktop.java
Thursday 23 Jun
4:02 pm

Ben Soares

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

Options
    • -45
    • +63
    /src/jalview/jbgui/APQHandlers.java
    • -2
    • +2
    /src/jalview/jbgui/GDesktop.java
3:28 pm

Ben Soares

JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void

Options
    • -49
    • +69
    /src/jalview/jbgui/APQHandlers.java
    • -2
    • +2
    /src/jalview/jbgui/GDesktop.java
Friday 17 Jun
5:10 pm

Ben Soares

JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

Options
    • -0
    • +5
    /src/jalview/jbgui/APQHandlers.java