Mateusz Warowny

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/StructureChooser.java
JAL-3690 - fixed state inconsistency when restarting the calcworker

JAL-3690 partially reworked AlignCalcManager

todo:

- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI

- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)

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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/api/PollableAlignCalcWorkerI.java
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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 - introduce shutdown method that cleans up manager's resources.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 Documentation for AlignCalcListener

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    /src/jalview/api/AlignCalcListener.java
JAL-3690 Catch and notify about worker cancellation separately.

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    /src/jalview/api/AlignCalcListener.java
JAL-3690 Fix concurrent modification exception when workers are cancelled

JAL-3690 Documentation for AlignCalcManagerI2

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    /src/jalview/api/AlignCalcManagerI2.java
JAL - 3690 AlignCalc rebuilt - WIP

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/workers/AlignCalcManager2.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/ws/jws2/Jws2ClientFactory.java
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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    /src/jalview/api/AlignCalcListener.java
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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/api/AlignCalcManagerI2.java
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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/appletgui/AlignViewport.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /src/jalview/workers/ColumnCounterSetWorker.java
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    /src/jalview/workers/ConsensusThread.java
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    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
JAL-3690 changed AWSThread to use Timer instead

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    /src/jalview/ws/AWSThread.java
JAL-3690 alternative servers menu fix

JAL-3690 alternative servers menu fix

JAL-3690 restore jws1 JPred

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    /src/jalview/gui/AlignFrame.java
JAL-3690 switching to CompletableFuture to allow chaining

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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-3690 mark JalviewChangeSupport as deprecated

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    /src/jalview/gui/JalviewChangeSupport.java
JAL-3690 refactoring web-services discovery

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/ServiceChangeListener.java
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    /src/jalview/ws/jws1/Discoverer.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJS_2112

Conflicts:

src/jalview/gui/Desktop.java

src/jalview/gui/Preferences.java

src/jalview/jbgui/GPreferences.java

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3683 retrieve job status to output stream

Merge branch 'feature/JAL-3515-slivka-preferences' into alpha/JAL-3066_Jalview_212_slivka-integration

update slivka client for j2s compatibility

JAL-6386 update slivka client for j2s compatibility

Implement simple media type recognition.

JAL-3515 Change to JvOptionPane wrapper

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    /src/jalview/gui/SlivkaPreferences.java
Should I have a single array containing url, status pairs? It sounds more reasonable as the url and status always go together.

Should I have a single array containing url, status pairs? It sounds more reasonable as the url and status always go together.

JAL-3515 Build a WSPreferences page for Slivka services.
JAL-3515 Build a WSPreferences page for Slivka services.