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Friday 24 Sep 2021
2:17 pm

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

JAL-3829 abstract essential TDB metadata from the user configurable data array displayed in the JTable

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    • +115
    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
2:08 pm

Mateusz Warowny

JAL-3878 Move WSJob instantiation out of WebService classes.

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    • +7
    /src/jalview/ws2/WSJob.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
Thursday 23 Sep 2021
8:19 pm

Ben Soares

JAL-3594 added BG and UoD logo and banner to splashscreens, and adjusted status text box

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    /gradle.properties
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    /utils/channels/default/images/jalview_getdown_background.png
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5:27 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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5:27 pm

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

Merge branch 'features/r2_11_2/JAL-3821_reinstate_patch' into develop

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5:26 pm

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

JAL-3821 less ambiguous base class name for EMBL and GenBank flat file parsers

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    • -0
    • +833
    /src/jalview/io/EMBLLikeFlatFile.java
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    • +1
    /src/jalview/io/EmblFlatFile.java
    • -833
    • +0
    /src/jalview/io/FlatFile.java
    • -1
    • +1
    /src/jalview/io/GenBankFile.java
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    • +1
    /test/jalview/io/GenBankFileTest.java
5:24 pm

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

JAL-3821 ported to refactored FlatFile parser

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    • -2
    • +67
    /src/jalview/io/FlatFile.java
5:00 pm

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

JAL-3821 failing test

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    • -0
    • +16
    /test/jalview/io/EmblFlatFileTest.java
3:26 pm

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

JAL-3692 JAL-3861 remove extra call to .parse() so we don’t process the file again

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    • -1
    • +0
    /src/jalview/ws/dbsources/EmblFlatfileSource.java
2:04 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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2:04 pm

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

Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop

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2:02 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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Wednesday 22 Sep 2021
8:02 pm

Ben Soares

JAL-3851 api_specification.md in progress

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    • -0
    • +40
    /doc/api_specification.md
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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    /src/jalview/analysis/AlignSeq.java
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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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    /src/jalview/analysis/GeneticCodes.java
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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
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    /src/jalview/datamodel/AlignmentAnnotation.java
  16. … 88 more files in changeset.
Tuesday 21 Sep 2021
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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    • +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
    • +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
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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
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    /src/jalview/io/StructureFile.java
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    • +15
    /test/jalview/datamodel/SequenceTest.java
    • -0
    • +4
    /test/jalview/ext/jmol/JmolParserTest.java
Monday 20 Sep 2021
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
5:39 pm

Mateusz Warowny

JAL-3878 Implement AlignmentOperation WIP

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    • +380
    /src/jalview/ws2/operations/AlignmentOperation.java
5:30 pm

Mateusz Warowny

JAL-3878 Create interface for web service operations

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    /src/jalview/ws2/operations/Operation.java
5:29 pm

Mateusz Warowny

JAL-3878 Implement slivka web service and discoverer.

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    /src/jalview/ws2/slivka/SlivkaWS.java
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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
5:21 pm

Mateusz Warowny

JAL-3878 Add web service executor class and instantiate for each alignment viewport.

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    /src/jalview/viewmodel/AlignmentViewport.java
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    /src/jalview/ws2/WebServiceExecutor.java
5:13 pm

Mateusz Warowny

JAL-3878 Create base interfaces for new web services.

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    /src/jalview/ws2/JalviewWebServiceI.java
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    /src/jalview/ws2/MenuEntryProviderI.java
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    /src/jalview/ws2/MsaMenuEntryProvider.java
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    /src/jalview/ws2/ResultSupplier.java
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    /src/jalview/ws2/WSJob.java
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    /src/jalview/ws2/WSJobID.java
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    /src/jalview/ws2/WSJobState.java
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    /src/jalview/ws2/WSJobStatus.java
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    /src/jalview/ws2/WSJobTrackerI.java
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    /src/jalview/ws2/WebServiceDiscoverer.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/WebServiceInfoUpdater.java
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    /src/jalview/ws2/WebServiceThreadListenerI.java
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    /src/jalview/ws2/WebServiceWorkerI.java
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    • +64
    /src/jalview/ws2/utils/WSJobList.java
4:23 pm

Mateusz Warowny

JAL-3878 Remove throws declaration from param store construction.

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    /src/jalview/ws/slivkaws/SlivkaDatastore.java
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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
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    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
2:56 pm

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

JAL-3829 updated response for P01308

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    /test/jalview/fts/threedbeacons/p01308_tdb_resp.txt