jalview

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Commits this week: 13
Total Committers: 73
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Commits this week: 13

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Wednesday 29 Sep 2021
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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    • -0
    • +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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    • -0
    • +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
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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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    • -136
    • +176
    /src/jalview/gui/AlignFrame.java
    • -77
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    /src/jalview/gui/Desktop.java
    • -15
    • +16
    /src/jalview/gui/SlivkaPreferences.java
    • -1
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    /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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    • -537
    • +385
    /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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    • -0
    • +5
    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
    • -12
    • +6
    /src/jalview/gui/StructureChooser.java
    • -0
    • +16
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
    • -2
    • +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.

Options
    • -2
    • +0
    /src/jalview/ws2/WebServiceI.java
    • -2
    • +8
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -0
    • +2
    /src/jalview/ws2/operations/Operation.java
    • -2
    • +1
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
    • -11
    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
3:04 pm

Mateusz Warowny

JAL-3878 Code reformatting.

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    • -4
    • +1
    /src/jalview/ws2/WSJobStatus.java
    • -5
    • +15
    /src/jalview/ws2/WebServiceDiscoverer.java
    • -34
    • +46
    /src/jalview/ws2/WebServiceExecutor.java
    • -13
    • +16
    /src/jalview/ws2/WebServiceI.java
    • -11
    • +21
    /src/jalview/ws2/WebServiceInfoUpdater.java
    • -2
    • +4
    /src/jalview/ws2/WebServiceWorkerI.java
    • -1
    • +6
    /src/jalview/ws2/operations/Operation.java
    • -28
    • +47
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
    • -38
    • +79
    /src/jalview/ws2/slivka/SlivkaWebService.java
2:49 pm

Mateusz Warowny

JAL-3878 Display results of completed alignment job

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    • -103
    • +480
    /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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    • -1
    • +1
    /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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    • -0
    • +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 ?

Options
    • -2
    • +45
    /src/jalview/gui/StructureChooser.java
    • -2
    • +31
    /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

Options
    • -0
    • +115
    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
    • -48
    • +1
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -2
    • +5
    /src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
2:08 pm

Mateusz Warowny

JAL-3878 Move WSJob instantiation out of WebService classes.

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    • -10
    • +7
    /src/jalview/ws2/WSJob.java
    • -1
    • +2
    /src/jalview/ws2/WebServiceI.java
    • -3
    • +6
    /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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    • -1
    • +1
    /gradle.properties
    • binary
    /utils/channels/default/images/jalview_getdown_background.png
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    /utils/channels/default/images/jalview_getdown_background.xcf
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    /utils/channels/default/images/jalview_getdown_background_error.png
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    /utils/channels/default/images/jalview_getdown_background_initialising.png
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    /utils/channels/jalviewjs/images/jalviewjs_getdown_background.png
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    /utils/channels/jalviewjs/images/jalviewjs_getdown_background_error.png
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    /utils/channels/jalviewjs/images/jalviewjs_getdown_background_initialising.png
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    /utils/channels/release/images/jalview_getdown_background.png
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    /utils/channels/release/images/jalview_getdown_background.xcf
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    /utils/channels/release/images/jalview_getdown_background_error.png
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    /utils/channels/release/images/jalview_getdown_background_initialising.png
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    /utils/channels/test-release/images/jalview_getdown_background.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_error.png
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    /utils/channels/test-release/images/jalview_test-release_getdown_background_initialising.png
5:27 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
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
    • -1
    • +1
    /src/jalview/io/EmblFlatFile.java
    • -833
    • +0
    /src/jalview/io/FlatFile.java
    • -1
    • +1
    /src/jalview/io/GenBankFile.java
    • -1
    • +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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    • -1
    • +3
    /src/jalview/analysis/AlignSeq.java
    • -4
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    /src/jalview/analysis/AlignmentUtils.java
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    • +3
    /src/jalview/analysis/AnnotationSorter.java
    • -1
    • +3
    /src/jalview/analysis/Conservation.java
    • -1
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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
    • -1
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    /src/jalview/bin/HiDPISetting.java
    • -4
    • +6
    /src/jalview/bin/Jalview.java
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    /src/jalview/bin/JalviewLite.java
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    /src/jalview/bin/Launcher.java
    • -1
    • +3
    /src/jalview/bin/MemorySetting.java
    • -2
    • +4
    /src/jalview/commands/ChangeCaseCommand.java
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    /src/jalview/commands/EditCommand.java
    • -1
    • +3
    /src/jalview/datamodel/AlignmentAnnotation.java
  16. … 88 more files in changeset.