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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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    • -8
    • +6
    /help/help/html/features/preferences.html
    • -3
    • +7
    /help/help/html/releases.html
    • -8
    • +10
    /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
    • +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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    • -0
    • +3
    /resources/lang/Messages.properties
    • -121
    • +246
    /src/jalview/gui/StructureChooser.java
    • -25
    • +32
    /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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    • -55
    • +225
    /utils/debian/build_gradle.patch
    • -141
    • +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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    • -1
    • +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 2021
5:48 pm

Ben Soares

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

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    • -0
    • +2739
    /utils/debian/build_gradle.patch
5:39 pm

Mateusz Warowny

JAL-3878 Implement AlignmentOperation WIP

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    • -0
    • +380
    /src/jalview/ws2/operations/AlignmentOperation.java
5:30 pm

Mateusz Warowny

JAL-3878 Create interface for web service operations

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    • -0
    • +13
    /src/jalview/ws2/operations/Operation.java
5:29 pm

Mateusz Warowny

JAL-3878 Implement slivka web service and discoverer.

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    • -175
    • +0
    /src/jalview/ws2/slivka/SlivkaWS.java
    • -0
    • +175
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
    • -0
    • +215
    /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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    • -0
    • +10
    /src/jalview/viewmodel/AlignmentViewport.java
    • -50
    • +86
    /src/jalview/ws2/WebServiceExecutor.java
5:13 pm

Mateusz Warowny

JAL-3878 Create base interfaces for new web services.

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    • -67
    • +0
    /src/jalview/ws2/JalviewWebServiceI.java
    • -2
    • +1
    /src/jalview/ws2/MenuEntryProviderI.java
    • -211
    • +0
    /src/jalview/ws2/MsaMenuEntryProvider.java
    • -0
    • +9
    /src/jalview/ws2/ResultSupplier.java
    • -0
    • +198
    /src/jalview/ws2/WSJob.java
    • -69
    • +0
    /src/jalview/ws2/WSJobID.java
    • -57
    • +0
    /src/jalview/ws2/WSJobState.java
    • -0
    • +103
    /src/jalview/ws2/WSJobStatus.java
    • -9
    • +0
    /src/jalview/ws2/WSJobTrackerI.java
    • -0
    • +58
    /src/jalview/ws2/WebServiceDiscoverer.java
    • -0
    • +53
    /src/jalview/ws2/WebServiceI.java
    • -0
    • +89
    /src/jalview/ws2/WebServiceInfoUpdater.java
    • -0
    • +14
    /src/jalview/ws2/WebServiceThreadListenerI.java
    • -53
    • +17
    /src/jalview/ws2/WebServiceWorkerI.java
    • -0
    • +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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    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaDatastore.java
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaParamSet.java
    • -7
    • +1
    /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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    • -1
    • +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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    • -32
    • +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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    • -1
    • +1
    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
    • -3
    • +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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    • -0
    • +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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    • -1
    • +1
    /resources/fts/tdbeacons_data_columns.txt
    • -0
    • +2
    /resources/lang/Messages.properties
    • -11
    • +86
    /src/jalview/gui/StructureChooser.java
    • -6
    • +18
    /src/jalview/gui/structurechooser/StructureChooserQuerySource.java
    • -2
    • +6
    /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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    • -5
    • +42
    /src/jalview/ext/jmol/JmolParser.java
    • -13
    • +18
    /src/mc_view/PDBChain.java
    • -2
    • +2
    /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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    • -9
    • +25
    /src/jalview/datamodel/PDBEntry.java
    • -1
    • +1
    /test/jalview/datamodel/PDBEntryTest.java
    • -1
    • +1
    /test/mc_view/PDBChainTest.java
Friday 17 Sep 2021
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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    • -32
    • +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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    • -32
    • +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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