jalview

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Commits this week: 38
Total Committers: 72
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Commits this week: 38

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Wednesday 22 Sep
12:08 am

Ben Soares

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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    • -1
    • +3
    /src/jalview/analysis/AlignSeq.java
    • -4
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/AnnotationSorter.java
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    /src/jalview/analysis/Conservation.java
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    /src/jalview/analysis/Finder.java
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    • +7
    /src/jalview/analysis/GeneticCodes.java
    • -2
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    /src/jalview/analysis/SequenceIdMatcher.java
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    /src/jalview/bin/HiDPISetting.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/bin/JalviewLite.java
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    /src/jalview/bin/Launcher.java
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    /src/jalview/bin/MemorySetting.java
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    /src/jalview/commands/ChangeCaseCommand.java
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    /src/jalview/commands/EditCommand.java
    • -1
    • +3
    /src/jalview/datamodel/AlignmentAnnotation.java
  16. … 88 more files in changeset.
Tuesday 21 Sep
9:59 pm

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

JAL-3746 release notes and what’s new for 2.11.2 - in progress

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    /help/help/html/features/preferences.html
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    /help/help/html/releases.html
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    /help/help/html/whatsNew.html
4:24 pm

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

Merge branch 'doc/JAL-3746_Release_2_11_2' into develop

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    • -4
    • +4
    /src/jalview/gui/AlignFrame.java
2:24 pm

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

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

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1:54 pm

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

JAL-3829 - callback finessing - leave DBRefFetcher to do progress updates itself

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    • -28
    • +21
    /src/jalview/gui/StructureChooser.java
11:41 am

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

JAL-3829 prefix PDBe filters with PDBe to make clear what they search

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    • +5
    /src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
11:36 am

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

JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched

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    • +3
    /resources/lang/Messages.properties
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    • +246
    /src/jalview/gui/StructureChooser.java
    • -25
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    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
9:57 am

Ben Soares

JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing doc/*.html and build_properties from source tarball.

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    • +225
    /utils/debian/build_gradle.patch
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    • +10
    /utils/debian/debian_build.gradle
8:30 am

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

JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry

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    • +37
    /src/jalview/datamodel/PDBEntry.java
    • -0
    • +1
    /src/jalview/io/StructureFile.java
    • -0
    • +15
    /test/jalview/datamodel/SequenceTest.java
    • -0
    • +4
    /test/jalview/ext/jmol/JmolParserTest.java
Monday 20 Sep
5:48 pm

Ben Soares

JAL-3521 Created a patch file to transform build.gradle into debian_build.gradle

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    • +2739
    /utils/debian/build_gradle.patch
2:56 pm

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

JAL-3829 updated response for P01308

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    • +1
    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt
2:56 pm

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

JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality

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    • +52
    /src/jalview/gui/StructureChooser.java
    • -0
    • +22
    /test/jalview/gui/StructureChooserTest.java
2:55 pm

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

JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession

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    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
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    • +5
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
2:54 pm

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

JAL-3829 throw the exception even if it has no message

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    • -14
    • +15
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
2:54 pm

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

JAL-3829 ensure nulls are not wildcards when retrieving annotation by calcId/label/description

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    • -6
    • +4
    /src/jalview/datamodel/Sequence.java
2:25 pm

Ben Soares

JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem

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    • -6
    • +31
    /utils/debian/debian_build.gradle
1:11 pm

Ben Soares

JAL-3521 not quite working minimal build.gradle for debian and 2.11.2

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    • +620
    /utils/debian/debian_build.gradle
11:19 am

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

JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

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    /resources/fts/tdbeacons_data_columns.txt
    • -0
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    /resources/lang/Messages.properties
    • -11
    • +86
    /src/jalview/gui/StructureChooser.java
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    • +18
    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
    • -2
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    /src/jalview/gui/structurechooser/TDBResultAnalyser.java
    • -35
    • +72
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
11:16 am

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

JAL-3829 make sure structure data type reflects actual format identified

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    • +42
    /src/jalview/ext/jmol/JmolParser.java
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    • +18
    /src/mc_view/PDBChain.java
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    /src/mc_view/PDBfile.java
11:14 am

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

JAL-3829 store 3db metadata on PDBEntry so it can be shown in Cache/etc

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    • -3
    • +61
    /src/jalview/datamodel/PDBEntry.java
11:13 am

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

JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file

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    • +25
    /src/jalview/datamodel/PDBEntry.java
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    • +1
    /test/jalview/datamodel/PDBEntryTest.java
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    • +1
    /test/mc_view/PDBChainTest.java
Saturday 18 Sep
9:54 am

Jim Procter

Friday 17 Sep
6:16 pm

Ben Soares

Merge branch 'merge/develop_JAL-1260' into develop

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6:11 pm

Ben Soares

JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

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    • +14
    /src/jalview/io/GenBankFile.java
6:11 pm

Ben Soares

JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

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    • +14
    /src/jalview/io/GenBankFile.java
5:42 pm

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

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

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5:39 pm

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

JAL-3079 JAL-3055 remember to reset font transform after rendering logo

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    • +2
    /src/jalview/renderer/AnnotationRenderer.java
4:38 pm

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

JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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    /THIRDPARTYLIBS
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    /build.gradle
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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
    • binary
    /j8lib/Jmol-14.31.53.jar
1:13 pm

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

JAL-2226 transfer chain annotation when calcId, label and description are distinct - so annotations from multiple chains and structures are all shown.

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    • +11
    /src/mc_view/PDBChain.java
1:12 pm

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

JAL-2226 new method to search for annotation matching particular description as well as calcId and label

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /test/jalview/datamodel/SequenceTest.java