jalview

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Total Committers: 73
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Commits this week: 8

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Friday 01 Oct 2021
12:35 pm

Ben Soares

Merge branch 'improvement/JAL-3594_logos_for_jalview_test' into develop

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12:32 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

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12:31 pm

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

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

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12:28 pm

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

JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

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    • -1
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    /resources/lang/Messages.properties
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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
12:10 pm

Ben Soares

Merge branch 'develop' into improvement/JAL-3594_logos_for_jalview_test

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12:08 pm

Ben Soares

JAL-3594 New Jalview Test logos and .icns/.ico creation helper script

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    /doc/README-DMG_background_image_creation.md
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    /doc/README-DMG_creation.md
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    /doc/README_convert_PNG_to_ICNS_and_ICO
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    /utils/channels/release/images/jalview_logo.svg
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    /utils/channels/test-release/images/jalview_test-release_banner.xcf
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    /utils/channels/test-release/images/jalview_test-release_getdown_background.png
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    /utils/channels/test-release/images/jalview_test-release_getdown_background.xcf
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    /utils/channels/test-release/images/jalview_test-release_getdown_background_error.png
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    /utils/channels/test-release/images/jalview_test-release_getdown_background_initialising.png
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    /utils/channels/test-release/images/jalview_test-release_logo-84.png
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    /utils/channels/test-release/images/jalview_test-release_logo-88.png
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    /utils/channels/test-release/images/jalview_test-release_logo.icns
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    /utils/channels/test-release/images/jalview_test-release_logo.ico
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    /utils/channels/test-release/images/jalview_test-release_logo.png
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    /utils/channels/test-release/images/jalview_test-release_logo.svg
  16. … 15 more files in changeset.
10:35 am

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

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

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    /src/jalview/gui/StructureChooser.java
12:16 am

Ben Soares

JAL-3594 Changed logo for Jalview Test

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    /utils/channels/test-release/channel_gradle.properties
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    /utils/channels/test-release/images/jalview_getdown_background.xcf
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    /utils/channels/test-release/images/jalview_logo.icns
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    /utils/channels/test-release/images/jalview_logo.ico
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    /utils/channels/test-release/images/jalview_logo.png
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    /utils/channels/test-release/images/jalview_logo.svg
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    /utils/channels/test-release/images/jalview_test-release_banner.xcf
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    /utils/channels/test-release/images/jalview_test-release_getdown_background.png
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    /utils/channels/test-release/images/jalview_test-release_getdown_background.xcf
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    /utils/channels/test-release/images/jalview_test-release_getdown_background_error.png
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    /utils/channels/test-release/images/jalview_test-release_getdown_background_initialising.png
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    /utils/channels/test-release/images/jalview_test-release_logo.icns
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    /utils/channels/test-release/images/jalview_test-release_logo.ico
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    /utils/channels/test-release/images/jalview_test-release_logo.svg
  16. … 21 more files in changeset.
12:08 am

Ben Soares

JAL-1260 Added .gbk to GenBank extensions. Added GenBank extensions to the installer.

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    /src/jalview/io/FileFormat.java
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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
Thursday 30 Sep 2021
5:26 pm

Mateusz Warowny

JAL-3878 Skip getting results of failed jobs.

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    /src/jalview/ws2/operations/AlignmentOperation.java
4:08 pm

Mateusz Warowny

JAL-3878 Add job log messages reporting.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
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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    /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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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws2/operations/AlignmentOperation.java
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    /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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    /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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    /src/jalview/io/FileFormat.java
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    /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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    • -1
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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

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    /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