jalview

Clone Tools

Stats

Commits this week: 3
Total Committers: 73
Last Commit:
Commits this week: 3

Lines of code count not available

Commit Activity

Commits By Day In Week
52 week commits volume
Commits By Day In Week
Commits by day
Commits By Day In Week
Commits by hour
Commits By Hour In Day
Commit calendar
 

Most active committers (90 days)

loading
loading
  • last updated a few seconds ago
All Commits Reviews
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
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
Monday 18 Apr
10:31 am

Ben Soares

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

Options
    • -3
    • +3
    /src/jalview/fts/core/GFTSPanel.java
    • -7
    • +7
    /src/jalview/gui/AlignFrame.java
    • -2
    • +2
    /src/jalview/gui/AlignViewport.java
    • -3
    • +3
    /src/jalview/gui/AnnotationChooser.java
    • -2
    • +2
    /src/jalview/gui/AnnotationColourChooser.java
    • -2
    • +2
    /src/jalview/gui/AnnotationColumnChooser.java
    • -3
    • +3
    /src/jalview/gui/AnnotationExporter.java
    • -2
    • +2
    /src/jalview/gui/AnnotationRowFilter.java
    • -2
    • +2
    /src/jalview/gui/AppVarna.java
    • -13
    • +15
    /src/jalview/gui/AquaInternalFrameManager.java
    • -3
    • +3
    /src/jalview/gui/CalculationChooser.java
    • -2
    • +2
    /src/jalview/gui/ChimeraViewFrame.java
    • -22
    • +35
    /src/jalview/gui/Desktop.java
    • -3
    • +3
    /src/jalview/gui/FeatureSettings.java
    • -5
    • +5
    /src/jalview/gui/Finder.java
  16. … 26 more files in changeset.
Thursday 07 Apr
12:35 am

Ben Soares

JAL-3991 Made info displayed only when needed (Java 11+)

Options
    • -2
    • +6
    /src/jalview/gui/Desktop.java
12:28 am

Ben Soares

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.

Options
    • -2
    • +3
    /src/jalview/gui/Desktop.java
12:08 am

Ben Soares

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.

Options
    • -0
    • +1
    /build.gradle
    • -0
    • +3
    /resources/lang/Messages.properties
    • -0
    • +4
    /resources/lang/Messages_es.properties
    • -0
    • +5
    /src/jalview/bin/Cache.java
    • -0
    • +41
    /src/jalview/bin/Jalview.java
    • -2
    • +9
    /src/jalview/bin/Launcher.java
    • -0
    • +113
    /src/jalview/util/LaunchUtils.java
Tuesday 05 Apr
6:37 pm

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

JAL-3981 patch tests and remove errant imports

Options
    • -4
    • +1
    /src/jalview/io/SequenceAnnotationReport.java
    • -13
    • +22
    /test/jalview/io/SequenceAnnotationReportTest.java
6:14 pm

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

JAL-3990 gradle spotlessApply

Options
    • -1
    • +2
    /src/jalview/gui/structurechooser/TDBResultAnalyser.java
    • -3
    • +3
    /src/jalview/io/SequenceAnnotationReport.java
    • -6
    • +4
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -4
    • +2
    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
6:12 pm

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

JAL-3990 release notes for 2.11.2.1 patch release

Options
    • -5
    • +10
    /help/help/html/releases.html
5:57 pm

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

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

Options
Thursday 31 Mar
8:44 pm

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

JAL-3983 release note for JAL-3985

Options
    • -0
    • +4
    /help/help/html/releases.html
8:42 pm

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

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

Options
3:17 pm

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

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

Options
    • -343
    • +362
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -5
    • +13
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -1
    • +1
    /test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt
    • -0
    • +1
    /test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt
    • -1
    • +0
    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
    • -0
    • +2
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1.txt
    • -0
    • +2506
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1_resp.txt
    • -0
    • +2
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2.txt
    • -0
    • +2520
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2_resp.txt
    • -0
    • +1
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3.txt
    • -0
    • +2517
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3_resp.txt
    • -0
    • +1
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4.txt
    • -0
    • +793
    /test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4_resp.txt
    • -0
    • +1
    /test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt
    • -0
    • +1
    /test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt
    • -13
    • +132
    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
2:06 pm

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

JAL-3985 formatting

Options
    • -0
    • +3
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
2:06 pm

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

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

Options
    • -26
    • +62
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
Wednesday 30 Mar
6:35 pm

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

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

Options
5:32 pm

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

JAL-3976 fix mock PDBFTS query & responses

Options
    • -1
    • +1
    /test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt
    • -1
    • +2377
    /test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt
4:56 pm

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

JAL-3983 known issue note for JAL-3984

Options
    • -0
    • +4
    /help/help/html/releases.html
4:54 pm

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

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

Options
    • -2
    • +2
    /help/help/html/releases.html
4:52 pm

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

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

Options
4:51 pm

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

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

Options
    • -7
    • +7
    /src/jalview/gui/TextColourChooser.java
4:23 pm

Jim Procter

4:22 pm

Jim Procter

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...