Mateusz Warowny

Merge branch 'JAL-3927_ws_preferences_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'update/JAL-3066_updated_testng' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3878 Use annotations from the representative sequence in the new alignment.

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    • +3
    /src/jalview/ws2/gui/JPredMenuBuilder.java
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    /src/jalview/ws2/operations/JPredWorker.java
JAL-3927 Make url checks asynchronous in preferences dialog

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    /src/jalview/gui/SlivkaPreferences.java
JAL-3878 Add jpred operation and worker to the services.

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    /src/jalview/ws2/gui/JPredMenuBuilder.java
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    • +35
    /src/jalview/ws2/operations/JPredOperation.java
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    /src/jalview/ws2/operations/JPredWorker.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Make openEditsParamsDialog an interface static method.

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    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
    • -0
    • +43
    /src/jalview/ws2/gui/MenuEntryProviderI.java
JAL-3066 Fix ambiguous assertEquals casting values to double.

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    /test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
JAL-3878 Add annotation operation and worker to the services.

    • -0
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    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
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    • +50
    /src/jalview/ws2/gui/ProgressBarUpdater.java
    • -0
    • +602
    /src/jalview/ws2/operations/AnnotationWorker.java
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    • +35
    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Handle nulls when filtering annotation workers by name.

JAL-3878 Move common poll method to upper class AbstractWorker

JAL-3878 Add methods to get and remove workers by their calc name.

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    /src/jalview/api/AlignCalcManagerI2.java
JAL-3878 Add multiple sequence operation.

    • -0
    • +206
    /src/jalview/ws2/gui/AlignmentMenuBuilder.java
    • -0
    • +170
    /src/jalview/ws2/gui/AlignmentProgressUpdater.java
    • -0
    • +145
    /src/jalview/ws2/gui/WebServiceInfoUpdater.java
    • -0
    • +415
    /src/jalview/ws2/operations/AlignmentWorker.java
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    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Create abstract workers and their utility classes.

    • -0
    • +75
    /src/jalview/ws2/operations/AbstractPollableWorker.java
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    /src/jalview/ws2/operations/AbstractWorker.java
    • -0
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/operations/WSJobList.java
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    /src/jalview/ws2/operations/WebServiceWorkerI.java
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    /src/jalview/ws2/operations/WebServiceWorkerListener.java
JAL-3878 Create pollable task and executor it can be run with.

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    /src/jalview/ws2/PollableTaskI.java
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    /src/jalview/ws2/PollableTaskListenerI.java
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    /src/jalview/ws2/PollingTaskExecutor.java
JAL-3878 Add ws menu builder and attach to the align frame.

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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceDiscovererI.java
    • -0
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    /src/jalview/ws2/gui/WebServicesMenuBuilder.java
JAL-3878 Add slivka's implementations of web service and discoverer.

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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Create backbone for new web services

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    /src/jalview/ws2/WSJob.java
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    /src/jalview/ws2/WSJobStatus.java
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    /src/jalview/ws2/WebServiceDiscovererI.java
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    /src/jalview/ws2/WebServiceI.java
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    • +28
    /src/jalview/ws2/gui/MenuEntryProviderI.java
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    • +144
    /src/jalview/ws2/operations/AbstractOperation.java
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    • +119
    /src/jalview/ws2/operations/Operation.java
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    • +97
    /src/jalview/ws2/operations/OperationStub.java
JAL-3066 Remove redundant throws declaration from SlivkaParamSet constructor.

    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3878 Add RNAalifold service discovery.

Merge branch 'JAL-3866_RNAalifold-slivka-client' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'alpha/JAL-3899_deuniquify_refactor' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3878 Add javadocs to created classes and reformat code.

    • -6
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    /src/jalview/gui/WebServicesMenuBuilder.java
    • -0
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    /src/jalview/ws2/MenuEntryProviderI.java
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    • +39
    /src/jalview/ws2/PollableTaskI.java
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    /src/jalview/ws2/PollableTaskListenerI.java
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    • +39
    /src/jalview/ws2/PollingTaskExecutor.java
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    /src/jalview/ws2/ResultSupplier.java
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    • +101
    /src/jalview/ws2/WebServiceDiscoverer.java
    • -0
    • +11
    /src/jalview/ws2/WebServiceInfoUpdater.java
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    /src/jalview/ws2/WebServiceWorkerI.java
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    /src/jalview/ws2/gui/ProgressBarUpdater.java
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    • +84
    /src/jalview/ws2/operations/Operation.java
JAL-3878 Remove redundand edit params dialog method from the AnnotationOperation.

JAL-3878 Separate gui elements from operations.

Separation went well for alignment operation but not so much

for the annotations. GUI progress bar needs to be moved outside

the operation and be controlled by the worker listener.

Addition of the results to the frame needs to be moved out from

the #done method, but it's strongly wired to the align frame

code and cannot be nicely packed into AnnotationResult object.

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    /src/jalview/ws2/WebServiceDiscoverer.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/WebServiceWorkerListener.java
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    • +73
    /src/jalview/ws2/WebServiceWorkerListenersList.java
    • -0
    • +377
    /src/jalview/ws2/gui/AlignmentMenuBuilder.java
    • -0
    • +190
    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
    • -0
    • +8
    /src/jalview/ws2/operations/Operation.java
    • -22
    • +2
    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Make interactive service arguments persistent between starts.

JAL-3878 Create proper menu for interactive services.

JAL-3878 Add methods to get and remove workers by their calc name.

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    /src/jalview/api/AlignCalcManagerI2.java
JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

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    • +201
    /src/jalview/gui/WebServicesMenuBuilder.java
JAL-3878 Annotation comments and questions

JAL-3878 Add annotation operations to slivka discoverer.