jalview

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Commits this week: 17
Total Committers: 73
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Commits this week: 17

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Monday 08 Aug
6:49 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:48 pm

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

JAL-4046 release on 9th August 2022

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    /help/markdown/releases/release-2_11_2_4.md
6:31 pm

Jim Procter

6:28 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:28 pm

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

JAL-4046 JAL-3993 imports reformatting

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    /src/jalview/gui/SliderPanel.java
6:27 pm

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

JAL-4046 JAL-3993 patch for 2.11.2.4 release

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    /help/markdown/releases/release-2_11_2_4.md
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    /src/jalview/gui/SliderPanel.java
6:09 pm

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

JAL-4046 release notes for JAL-3991

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    /help/markdown/releases/release-2_11_2_4.md
6:01 pm

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

Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop

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    /build.gradle
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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/Desktop.java
5:54 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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5:50 pm

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

JAL-4046 release notes for JAL-4014 - gecos colourschemes

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    /help/markdown/releases/release-2_11_2_4.md
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    /help/markdown/whatsnew/whatsnew-2_11_2_4.md
5:16 pm

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

Merge branch 'improvement/JAL-4014_gecos_colour_schemes' into develop

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5:07 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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5:06 pm

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

JAL-4056 documented in release notes for JAL-4043

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    /help/markdown/releases/release-2_11_2_4.md
4:46 pm

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

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

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    /resources/lang/Messages.properties
4:42 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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4:42 pm

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

JAL-4043 what’s new, updated help images and release notes for JAL-4034 (3d beacons button)

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    /help/help/html/features/3dbeacons_button.png
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    /help/help/html/features/schooser_main.png
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    /help/markdown/releases/release-2_11_2_4.md
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    /help/markdown/whatsnew/whatsnew-2_11_2_4.md
4:17 pm

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

JAL-4034 show the loading spinner when switching between tabs

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    /src/jalview/gui/StructureChooser.java
2:47 pm

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

Merge branch 'features/JAL-4034_improve_3dbeacons_button_and_ux' into develop

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Monday 01 Aug
11:32 am

Ben Soares

JAL-4056 fixed tl;dr section of doc/building.md

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    /doc/building.md
Friday 29 Jul
11:36 am

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

JAL-4055 quick patch to see how Jalview looks as a free-floating multiwindowed app rather than a Desktop contained app

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    /src/jalview/gui/Desktop.java
Thursday 28 Jul
6:05 pm

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

JAL-4048 feature group filter

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    /src/jalview/viewmodel/seqfeatures/IdColumns.java
Tuesday 26 Jul
6:01 pm

Ben Soares

JAL-4036 Fixed the virus_host_id query field

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    /resources/fts/uniprot_data_columns-2022.txt
6:01 pm

Ben Soares

JAL-4036 Added text to help about different number and date range acceptable formats

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    /help/help/html/features/uniprotsequencefetcher.html
Monday 25 Jul
5:09 pm

Ben Soares

JAL-4036 updated help about new UniProt API

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    /help/help/html/features/uniprotqueryfields.html
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    /help/help/html/features/uniprotsequencefetcher.html
11:00 am

Ben Soares

JAL-4036 moved a comment block

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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
10:57 am

Ben Soares

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

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    /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

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    /src/jalview/jbgui/GStructureChooser.java
Friday 22 Jul
6:17 pm

Ben Soares

JAL-4036 Changes made from code review CR-JAL-265

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    /src/jalview/fts/core/GFTSPanel.java
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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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    /src/jalview/fts/service/uniprot/UniprotFTSPanel.java
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.

4:37 pm

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

JAL-4048 fix disappearing sequence IDs, and non-positional feature descriptions

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    /src/jalview/gui/IdCanvas.java
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    /src/jalview/viewmodel/seqfeatures/IdColumns.java