jalview

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Commits this week: 7
Total Committers: 73
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Commits this week: 7

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Thursday 30 Sep 2021
9:35 am

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

JAL-2909 pass a dummy sequence object to receive features. Ideally we should test that features look like they are expected too here !

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    /test/jalview/datamodel/CigarParserTest.java
9:18 am

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

JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop Merge remote-tracking branch 'origin/features/JAL-2909_bamImport2_11' into features/JAL-2909_bamImport_2_11_2

Conflicts:

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/FileFormat.java

src/jalview/io/FileLoader.java

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    /resources/lang/Messages.properties
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    /src/jalview/io/AlignFile.java
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    /src/jalview/io/AlignmentFileReaderI.java
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    /src/jalview/io/AppletFormatAdapter.java
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    /src/jalview/io/FileFormat.java
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    /src/jalview/io/FileLoader.java
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    /src/jalview/io/FileParse.java
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    /src/jalview/io/FormatAdapter.java
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    /src/jalview/io/IdentifyFile.java
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    /utils/checkstyle/import-control.xml
Wednesday 29 Sep 2021
8:51 pm

Ben Soares

JAL-3885 Made the database JComboBox have StringPair entries to allow a display value, set to the single item dbname if there's a single item

Options
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    • +112
    /src/jalview/gui/SequenceFetcher.java
3:50 pm

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

JAL-3884 squish alarming but harmless errors when uniprot doesn’t have a record

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    /src/jalview/ws/dbsources/Uniprot.java
3:37 pm

Mateusz Warowny

JAL-3878 Add isInteractive() method to Operation interface.

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    /src/jalview/ws2/operations/AlignmentOperation.java
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    /src/jalview/ws2/operations/Operation.java
3:32 pm

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

JAL-3881 split on any nonalphanumeric symbol (plus _) to generate putative sequence identifiers with which to query databases

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    /src/jalview/ws/DBRefFetcher.java
3:30 pm

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

JAL-3829 report when 3d-beacons doesn’t provide any models

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    /resources/lang/Messages.properties
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    /src/jalview/gui/StructureChooser.java
2:45 pm

Mateusz Warowny

JAL-3878 Add getName() to Operation interface.

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    /src/jalview/ws2/operations/AlignmentOperation.java
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    /src/jalview/ws2/operations/Operation.java
Tuesday 28 Sep 2021
4:09 pm

Ben Soares

JAL-3783 Updated groovy-all-2.4. Currently newer stable releases cause a problem with shadowJar.

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    /j11lib/groovy-all-2.4.12-indy.jar
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    /j11lib/groovy-all-2.4.21-indy.jar
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    /j8lib/groovy-all-2.4.12-indy.jar
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    /j8lib/groovy-all-2.4.21-indy.jar
Monday 27 Sep 2021
3:03 pm

Mateusz Warowny

JAL-3878 Wire web services logic to UI elements.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/operations/AlignmentOperation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
2:29 pm

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

JAL-3746 update the example corefile for jalviewjs

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    /utils/jalviewjs/classlists/jvexamplefile.txt
Friday 24 Sep 2021
5:23 pm

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

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

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    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
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    /src/jalview/jbgui/GStructureChooser.java
5:05 pm

Mateusz Warowny

JAL-3878 Fire service changed event after discovery task is done.

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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
5:05 pm

Mateusz Warowny

JAL-3878 Fix incorrect value of isRunning in SlivkaWSDiscoverer

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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
4:19 pm

Mateusz Warowny

JAL-3878 Move operation type from WebService to Operation.

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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/operations/AlignmentOperation.java
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
3:04 pm

Mateusz Warowny

JAL-3878 Code reformatting.

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    /src/jalview/ws2/WSJobStatus.java
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    /src/jalview/ws2/WebServiceDiscoverer.java
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    /src/jalview/ws2/WebServiceExecutor.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/WebServiceWorkerI.java
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
2:49 pm

Mateusz Warowny

JAL-3878 Display results of completed alignment job

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    /src/jalview/ws2/operations/AlignmentOperation.java
2:43 pm

Mateusz Warowny

JAL-3878 Change SERVER_ERROR.isSubmitted to false.

Some server errors may occur before the job is submitted.

It's safer to associate the error with the job not being

submitted.

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    /src/jalview/ws2/WSJobStatus.java
2:23 pm

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

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

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2:23 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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2:22 pm

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

JAL-3821 data file for failing test

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    /test/jalview/io/J03321_rna.embl.txt
2:19 pm

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

JAL-3829 right click to view popup menu to show link - maybe better to have a link button in the table instead ?

Options
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
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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    /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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    /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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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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    /src/jalview/io/EMBLLikeFlatFile.java
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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/io/FlatFile.java
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    /src/jalview/io/GenBankFile.java
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    /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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    /src/jalview/io/FlatFile.java
5:00 pm

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

JAL-3821 failing test

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    /test/jalview/io/EmblFlatFileTest.java