jalview

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Thursday 30 Sep 2021
4:07 pm

Mateusz Warowny

JAL-3878 Fix null pointer exception when preparing empty sequences for job.

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    /src/jalview/ws2/operations/AlignmentOperation.java
3:38 pm

Mateusz Warowny

JAL-3878 Fetch sequences for alignment on menu action, not creation.

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    • +22
    /src/jalview/ws2/operations/AlignmentOperation.java
1:23 pm

Mateusz Warowny

JAL-3878 Split web services menu entries by programs and hosts.

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    • -1
    • +21
    /src/jalview/gui/AlignFrame.java
    • -0
    • +6
    /src/jalview/ws2/operations/AlignmentOperation.java
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    • +2
    /src/jalview/ws2/operations/Operation.java
11:19 am

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

Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed' into develop

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10:39 am

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

JAL-2909 increase commandlinetests timeout

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    • +2
    /test/jalview/bin/CommandLineOperations.java
10:30 am

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

JAL-2909 fix up tests and ensure we don’t test bam as a writable format

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    • -1
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    /src/jalview/io/FileFormat.java
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    • +4
    /test/jalview/io/FileFormatsTest.java
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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    • +4
    /resources/lang/Messages.properties
    • -5
    • +14
    /src/jalview/io/AlignFile.java
    • -0
    • +11
    /src/jalview/io/AlignmentFileReaderI.java
    • -3
    • +15
    /src/jalview/io/AppletFormatAdapter.java
    • -0
    • +21
    /src/jalview/io/FileFormat.java
    • -2
    • +39
    /src/jalview/io/FileLoader.java
    • -1
    • +2
    /src/jalview/io/FileParse.java
    • -1
    • +0
    /src/jalview/io/FormatAdapter.java
    • -2
    • +9
    /src/jalview/io/IdentifyFile.java
    • -0
    • +5
    /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
    • -42
    • +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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    • -11
    • +21
    /src/jalview/ws/dbsources/Uniprot.java
3:37 pm

Mateusz Warowny

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

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    • +6
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -0
    • +2
    /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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    • -4
    • +8
    /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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    • +2
    /resources/lang/Messages.properties
    • -1
    • +7
    /src/jalview/gui/StructureChooser.java
2:45 pm

Mateusz Warowny

JAL-3878 Add getName() to Operation interface.

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    • +6
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -0
    • +2
    /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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    • binary
    /j11lib/groovy-all-2.4.12-indy.jar
    • binary
    /j11lib/groovy-all-2.4.21-indy.jar
    • binary
    /j8lib/groovy-all-2.4.12-indy.jar
    • binary
    /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
    • -77
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    /src/jalview/gui/Desktop.java
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    /src/jalview/gui/SlivkaPreferences.java
    • -1
    • +0
    /src/jalview/ws2/WebServiceExecutor.java
    • -7
    • +30
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -19
    • +14
    /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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    • +5
    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
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    • +6
    /src/jalview/gui/StructureChooser.java
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    • +16
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
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    • +2
    /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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    • -1
    • +1
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
5:05 pm

Mateusz Warowny

JAL-3878 Fix incorrect value of isRunning in SlivkaWSDiscoverer

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    • -2
    • +2
    /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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    • +306
    /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 ?

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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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    • +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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    /src/jalview/ws2/WSJob.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java