jalview

Clone Tools

Stats

Commits this week: 8
Total Committers: 73
Last Commit:
Commits this week: 8

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
Wednesday 15 Sep 2021
4:11 pm

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

JAL-3766 cut new patch release Conflicts: RELEASE

Options
    • -1
    • +18
    /help/help/html/releases.html
    • -5
    • +6
    /help/help/html/whatsNew.html
4:10 pm

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

JAL-3758 2.11.1.2 patch release notes and version bump Conflicts: RELEASE

Options
    • -0
    • +26
    /help/help/html/releases.html
4:09 pm

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

JAL-3741 http to https (and jar to jvp for exampleFile defaults!) Conflicts: src/jalview/bin/Jalview.java src/jalview/gui/Desktop.java

Options
    • -0
    • +1
    /help/help/help.jhm
    • -1
    • +2
    /help/help/helpTOC.xml
    • -1
    • +1
    /help/help/html/features/commandline.html
    • -4
    • +4
    /help/help/html/features/groovy.html
    • -4
    • +4
    /help/help/html/features/jvlfiles.html
    • -9
    • +11
    /help/help/html/features/search.html
    • binary
    /help/help/html/features/search.png
    • -9
    • +25
    /help/help/html/features/seqfetch.html
    • -1
    • +1
    /help/help/html/groovy/featuresCounter.html
    • -3
    • +8
    /help/help/html/index.html
    • -0
    • +212
    /help/help/html/logging.html
    • -1
    • +1
    /help/help/html/memory.html
    • -6
    • +103
    /help/help/html/releases.html
    • -3
    • +3
    /help/help/html/webServices/newsreader.html
    • -46
    • +50
    /help/help/html/whatsNew.html
  16. … 6 more files in changeset.
4:00 pm

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

JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

Options
    • -1
    • +10
    /help/help/html/features/clarguments.html
    • -3
    • +24
    /help/help/html/features/commandline.html
    • -1
    • +50
    /help/help/html/releases.html
3:56 pm

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

JAL-3675 version update and documentation for JAL-3493 JAL-3680 JAL-3638 Conflicts: RELEASE

Options
    • -4
    • +20
    /help/help/html/releases.html
3:55 pm

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

JAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in cursor mode. help/help/html/keys.html

Options
    • -1
    • +4
    /help/help/html/keys.html
    • -4
    • +4
    /src/jalview/gui/AlignFrame.java
    • -25
    • +58
    /src/jalview/gui/SeqPanel.java
3:51 pm

Ben Soares

Merge branch 'develop' into merge/develop_ben2

Options
7:34 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
7:34 am

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

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

Options
7:21 am

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
Tuesday 14 Sep 2021
7:10 pm

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

JAL-3829 parallel not welcome here

Options
    • -0
    • +1
    /test/jalview/gui/StructureChooserTest.java
6:59 pm

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

JAL-3829 test flakiness and human flakiness

Options
    • -20
    • +10
    /test/jalview/gui/StructureChooserTest.java
6:55 pm

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

JAL-3829 more info on test fail - seems to be flaky

Options
    • -2
    • +16
    /test/jalview/gui/StructureChooserTest.java
6:27 pm

Ben Soares

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Options
5:25 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
5:24 pm

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

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

Options
5:15 pm

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

JAL-3551 - doc tweak

Options
    • -1
    • +2
    /src/jalview/structures/models/AAStructureBindingModel.java
5:14 pm

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

JAL-3855 JAL-3829 better checks on PDB or mmCIF file based on URL path (though should really determine when processing via jmolData now we have mechanism) - ChimeraX in particular cares about file endings

Options
    • -1
    • +20
    /src/jalview/gui/StructureViewerBase.java
    • -1
    • +4
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
5:11 pm

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

JAL-3829 JAL-3855 moved routing for retrieving structures prior to opening a Jmol view to AppJmolBinding - this could be refactored further

Options
    • -132
    • +1
    /src/jalview/gui/AppJmol.java
    • -0
    • +139
    /src/jalview/gui/AppJmolBinding.java
    • -1
    • +10
    /src/jalview/gui/StructureViewerBase.java
5:01 pm

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

JAL-3829 JAL-3855 ignore case when detecting alphafold ID

Options
    • -2
    • +4
    /src/jalview/ws/dbsources/EBIAlfaFold.java
3:51 pm

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

JAL-3855 detect an alphafold model and import its temperature factor as reliability

Options
    • -2
    • +23
    /src/jalview/ext/jmol/JmolParser.java
    • -3
    • +15
    /src/mc_view/PDBChain.java
    • -1
    • +2
    /src/mc_view/PDBfile.java
    • -1
    • +1
    /test/mc_view/PDBChainTest.java
2:38 pm

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

JAL-3829 move mock query and responses to files

Options
    • -2764
    • +57
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
    • -1
    • +350
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -4
    • +19
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -0
    • +2
    /test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt
    • -0
    • +2381
    /test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt
    • -0
    • +1
    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
    • -2
    • +3
    /test/jalview/gui/StructureChooserTest.java
    • -2
    • +3
    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
1:36 pm

Ben Soares

Merge branch 'develop' into feature/JAL-2422ChimeraX

Options
1:36 pm

Ben Soares

JAL-2422 Also look in ~/Applications for ChimeraX on macOS

Options
    • -0
    • +6
    /src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
12:58 pm

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

Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Options
12:58 pm

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

Merge branch 'feature/JAL-2422ChimeraX' into develop

Options
12:36 pm

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

JAL-3829 3d-beacons doesn’t work as a sequence source just now

Options
    • -1
    • +2
    /src/jalview/ws/SequenceFetcher.java
12:36 pm

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

JAL-3829 avoid sending rubbish to PDBe search api

Options
    • -1
    • +5
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
12:35 pm

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

JAL-3829 some providers don’t provide model quality, some experimental methods don’t provide a resolution - try to leave these in their natural order

Options
    • -23
    • +79
    /src/jalview/gui/structurechooser/TDBResultAnalyser.java
12:34 pm

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

JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks

Options
    • -12
    • +21
    /src/jalview/fts/core/FTSRestClient.java
    • -7
    • +2394
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
    • -2
    • +2
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -0
    • +1
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -5
    • +13
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -8
    • +23
    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java