jalview

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Commits this week: 2
Total Committers: 73
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Commits this week: 2

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Friday 17 Sep 2021
1:05 pm

Ben Soares

JAL-3874 attempt to add source jars to eclipse through buildship

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    /build.gradle
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    /gradle.properties
    • binary
    /j11sources/Jmol-14.31.53-sources.jar
Thursday 16 Sep 2021
6:07 pm

Ben Soares

JAL-3779 Added to documentation

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    /help/help/html/features/annotationsFormat.html
1:53 pm

Ben Soares

JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Finder.java
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    /src/jalview/gui/SplitFrame.java
12:07 pm

Ben Soares

JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/OptsAndParamsPage.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/Jws2Client.java
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    /src/jalview/ws/jws2/MsaWSClient.java
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    /src/jalview/ws/jws2/dm/JabaOption.java
10:24 am

Ben Soares

JAL-3761 listToArray became rangeListToArray

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    /test/jalview/util/MappingUtilsTest.java
10:17 am

Ben Soares

JAL-3761 listToArray became rangeListToArray

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    /src/jalview/io/EmblFlatFile.java
Wednesday 15 Sep 2021
8:00 pm

Ben Soares

JAL-3818 formatting

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
5:19 pm

Ben Soares

Merge branch 'develop' into merge/develop_ben2

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5:16 pm

Ben Soares

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

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5:16 pm

Ben Soares

JAL-3829 Fixed Jmol jar -- duplicates of other classes were causing problem with shadow jar

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    /j11lib/Jmol-14.31.53-dedup.jar
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    /j11lib/Jmol-14.31.53.jar
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    /j8lib/Jmol-14.31.53-dedup.jar
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    /j8lib/Jmol-14.31.53.jar
5:06 pm

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

Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg' into develop

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    /src/jalview/util/Platform.java
3:51 pm

Ben Soares

Merge branch 'develop' into merge/develop_ben2

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7:34 am

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

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

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Tuesday 14 Sep 2021
7:10 pm

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

JAL-3829 parallel not welcome here

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    /test/jalview/gui/StructureChooserTest.java
6:59 pm

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

JAL-3829 test flakiness and human flakiness

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    /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

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    /test/jalview/gui/StructureChooserTest.java
6:27 pm

Ben Soares

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

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5:24 pm

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

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

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5:15 pm

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

JAL-3551 - doc tweak

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    /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

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    /src/jalview/gui/StructureViewerBase.java
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    /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

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    /src/jalview/gui/AppJmol.java
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    /src/jalview/gui/AppJmolBinding.java
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    /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

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    /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

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    /src/jalview/ext/jmol/JmolParser.java
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    /src/mc_view/PDBChain.java
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    /src/mc_view/PDBfile.java
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    /test/mc_view/PDBChainTest.java
2:38 pm

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

JAL-3829 move mock query and responses to files

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    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
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    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
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    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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    /test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt
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    /test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt
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    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
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    /test/jalview/gui/StructureChooserTest.java
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    /test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
1:36 pm

Ben Soares

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

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    /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

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12:58 pm

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

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

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12:36 pm

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

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

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    /src/jalview/ws/SequenceFetcher.java
12:36 pm

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

JAL-3829 avoid sending rubbish to PDBe search api

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    /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

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    /src/jalview/gui/structurechooser/TDBResultAnalyser.java