jalview

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Commits this week: 14
Total Committers: 73
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Commits this week: 14

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Today
5 hrs ago

Mateusz Warowny

JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

Options
    • -26
    • +9
    /src/jalview/gui/AlignFrame.java
    • -0
    • +201
    /src/jalview/gui/WebServicesMenuBuilder.java
11 hrs ago

Mateusz Warowny

JAL-3878 Annotation comments and questions

Options
    • -0
    • +5
    /src/jalview/ws2/operations/AnnotationOperation.java
    • -15
    • +37
    /src/jalview/ws2/operations/AnnotationServiceWorker.java
Tuesday 19 Oct
2:40 pm

Mateusz Warowny

JAL-3878 Add annotation operations to slivka discoverer.

Options
    • -0
    • +16
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
2:39 pm

Mateusz Warowny

JAL-3878 Fix sequences not being gathered when submitting without gaps.

Options
    • -0
    • +1
    /src/jalview/ws2/operations/AnnotationServiceWorker.java
2:33 pm

Mateusz Warowny

JAL-3878 Rename annotation provider method to getAnnotations

Options
    • -1
    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
2:31 pm

Mateusz Warowny

JAL-3878 Set job status to cancelled on job cancellation.

Despite job cancellation not being implemented in slivka client,

the job status should be updated to cancelled for the event to

be emitted to the ui updater.

Options
    • -0
    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
2:29 pm

Mateusz Warowny

JAL-3878 Start interactive job by registering them with calcManager

Options
    • -19
    • +26
    /src/jalview/ws2/operations/AnnotationOperation.java
2:25 pm

Mateusz Warowny

JAL-3878 Fix progress updater bar to account for cancelled state.

Options
    • -5
    • +2
    /src/jalview/ws2/gui/ProgressBarUpdater.java
Monday 18 Oct
5:04 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Refactoring SeqAnnotationServiceCalcWorker.

Options
    • -0
    • +5
    /src/jalview/ws2/WSJobStatus.java
    • -0
    • +47
    /src/jalview/ws2/gui/ProgressBarUpdater.java
    • -0
    • +18
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -84
    • +35
    /src/jalview/ws2/operations/AnnotationOperation.java
    • -0
    • +569
    /src/jalview/ws2/operations/AnnotationServiceWorker.java
    • -0
    • +6
    /src/jalview/ws2/operations/Operation.java
3:27 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
3:27 pm

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

Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu' into develop

Options
3:04 pm

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

JAL-3905 Fix: wait for response when sending mouseovers. Combined remove old label and add new label and also added warning in javadoc about out-of-order execution

Options
    • -7
    • +24
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -1
    • +4
    /src/jalview/structures/models/AAStructureBindingModel.java
1:18 pm

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

JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

Options
    • -4
    • +15
    /src/jalview/gui/ChimeraViewFrame.java
    • -2
    • +9
    /src/jalview/gui/PymolViewer.java
    • -1
    • +7
    /src/jalview/gui/StructureViewerBase.java
12:39 pm

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

JAL-3904 failing test

Options
    • -0
    • +6
    /src/jalview/api/structures/JalviewStructureDisplayI.java
    • -1
    • +5
    /src/jalview/gui/StructureViewerBase.java
    • -2
    • +30
    /test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
Wednesday 13 Oct
2:30 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Add getCalcName to AlignCalcWorkerI.

getCalcName() can be used to identify services that run the calculator.

when an alternative calculator (different host or parameters) is created

the old ones sharing the name can be stopped.

Options
    • -3
    • +15
    /src/jalview/api/AlignCalcWorkerI.java
    • -0
    • +6
    /src/jalview/workers/ColumnCounterSetWorker.java
    • -0
    • +6
    /src/jalview/workers/ComplementConsensusThread.java
    • -0
    • +6
    /src/jalview/workers/ConsensusThread.java
    • -0
    • +6
    /src/jalview/workers/ConservationThread.java
    • -0
    • +6
    /src/jalview/workers/InformationThread.java
    • -0
    • +6
    /src/jalview/workers/StrucConsensusThread.java
    • -1
    • +7
    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
    • -2
    • +9
    /test/jalview/workers/AlignCaclManager2Test.java
12:58 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Rename web service worker to more generic pollable task.

Options
    • -3
    • +3
    /src/jalview/viewmodel/AlignmentViewport.java
    • -0
    • +12
    /src/jalview/ws2/PollableTaskI.java
    • -0
    • +14
    /src/jalview/ws2/PollableTaskListenerI.java
    • -0
    • +126
    /src/jalview/ws2/PollingTaskExecutor.java
    • -133
    • +0
    /src/jalview/ws2/WebServiceExecutor.java
    • -14
    • +0
    /src/jalview/ws2/WebServiceThreadListenerI.java
    • -7
    • +3
    /src/jalview/ws2/WebServiceWorkerI.java
    • -4
    • +4
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -4
    • +4
    /src/jalview/ws2/operations/AnnotationOperation.java
Saturday 09 Oct
2:01 pm

Mateusz Warowny

Update annotation operation WIP

Options
    • -2
    • +3
    /src/jalview/ws2/operations/AnnotationOperation.java
Thursday 07 Oct
2:31 pm

Mateusz Warowny

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

Options
    • -1
    • +6
    /src/jalview/ws2/ResultSupplier.java
    • -1
    • +4
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -4
    • +22
    /src/jalview/ws2/slivka/SlivkaWebService.java
11:34 am

Mateusz Warowny

JAL-3899 Replace prints with logger messages.

Options
    • -10
    • +17
    /src/jalview/analysis/SeqsetUtils.java
Wednesday 06 Oct
5:32 pm

Mateusz Warowny

JAL-3899 Update usages of uniquify and deuniquify.

Options
    • -1
    • +2
    /src/jalview/datamodel/SeqCigar.java
    • -1
    • +3
    /src/jalview/hmmer/HMMAlign.java
    • -1
    • +3
    /src/jalview/hmmer/HMMBuild.java
    • -4
    • +6
    /src/jalview/hmmer/HmmerCommand.java
    • -1
    • +3
    /src/jalview/hmmer/Search.java
    • -4
    • +5
    /src/jalview/io/packed/JalviewDataset.java
    • -1
    • +2
    /src/jalview/ws/AWsJob.java
    • -6
    • +8
    /src/jalview/ws/jws1/JPredClient.java
    • -9
    • +11
    /src/jalview/ws/jws1/JPredThread.java
    • -6
    • +8
    /src/jalview/ws/jws2/JPredThread.java
    • -1
    • +2
    /src/jalview/ws/rest/RestJob.java
5:32 pm

Mateusz Warowny

tmp

Options
    • -1
    • +2
    /src/jalview/datamodel/SeqCigar.java
    • -1
    • +3
    /src/jalview/hmmer/HMMAlign.java
    • -1
    • +3
    /src/jalview/hmmer/HMMBuild.java
    • -4
    • +6
    /src/jalview/hmmer/HmmerCommand.java
    • -1
    • +3
    /src/jalview/hmmer/Search.java
    • -4
    • +5
    /src/jalview/io/packed/JalviewDataset.java
    • -1
    • +2
    /src/jalview/ws/AWsJob.java
    • -1
    • +2
    /src/jalview/ws/rest/RestJob.java
3:23 pm

Mateusz Warowny

JAL-3899 Refactor sequence de/uniquification.

Options
    • -103
    • +71
    /src/jalview/analysis/SeqsetUtils.java
    • -1
    • +2
    /test/jalview/analysis/SeqsetUtilsTest.java
Tuesday 05 Oct
6:53 pm

Ben Soares

JAL-3416 make flat default laf for linux

Options
    • -2
    • +2
    /src/jalview/bin/Jalview.java
5:07 pm

Mateusz Warowny

JAL-3878 Annotation operation skeleton.

Options
    • -0
    • +261
    /src/jalview/ws2/operations/AnnotationOperation.java
    • -0
    • +30
    /src/jalview/ws2/slivka/SlivkaWebService.java
Monday 04 Oct
8:13 pm

Ben Soares

JAL-3416 updated FlatLaf to 1.6 and added some tabbed pane properties

Options
    • binary
    /j11lib/flatlaf-0.46.jar
    • binary
    /j11lib/flatlaf-1.6.jar
    • binary
    /j8lib/flatlaf-1.6.jar
    • -0
    • +6
    /src/jalview/bin/Jalview.java
5:46 pm

Ben Soares

Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

Options
    • -11
    • +16
    /src/jalview/bin/Jalview.java
Friday 01 Oct
6:29 pm

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

JAL-2909 JAL-3894 hack in support to import regions of an unindexed SAM file.

Options
    • -1
    • +10
    /src/jalview/datamodel/CigarParser.java
    • -22
    • +64
    /src/jalview/io/BamFile.java
    • -1
    • +1
    /src/jalview/io/FileFormat.java
    • -0
    • +5
    /src/jalview/io/IdentifyFile.java
5:45 pm

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

Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

Options
    • -1
    • +3
    /resources/lang/Messages.properties
    • -1
    • +1
    /src/jalview/io/FileFormat.java
5:38 pm

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

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
5:36 pm

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

JAL-3616 show name of structure viewer in ‘new view’ button

Options
    • -0
    • +1
    /resources/lang/Messages.properties
    • -1
    • +7
    /src/jalview/gui/StructureViewer.java
    • -1
    • +5
    /src/jalview/jbgui/GStructureChooser.java