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JAL-3954 Prepare a skeleton for PHMMER web service.

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    ./PhmmerOperation.java
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JAL-3878 Use AlignViewport interface instead of concrete implementation in AlignmentWorker

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

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JAL-3878 Add jpred operation and worker to the services.

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    ./JPredOperation.java
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    ./JPredWorker.java
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JAL-3878 Add annotation operation and worker to the services.

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    ./AnnotationOperation.java
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    ./AnnotationWorker.java
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JAL-3878 Move common poll method to upper class AbstractWorker

JAL-3878 Add multiple sequence operation.

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    ./AlignmentOperation.java
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    ./AlignmentWorker.java
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JAL-3878 Create abstract workers and their utility classes.

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    ./AbstractPollableWorker.java
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    ./AbstractWorker.java
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    ./WebServiceWorkerI.java
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    ./WebServiceWorkerListener.java
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    ./WebServiceWorkerListenersList.java
JAL-3878 Create backbone for new web services

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    ./AbstractOperation.java
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    ./OperationStub.java
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JAL-3878 Add RNAalifold service discovery.

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

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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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JAL-3878 Make interactive service arguments persistent between starts.

JAL-3878 Create proper menu for interactive services.

JAL-3878 Annotation comments and questions

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

JAL-3878 Start interactive job by registering them with calcManager

JAL-3878 Refactoring SeqAnnotationServiceCalcWorker.

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

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Update annotation operation WIP

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

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JAL-3878 Annotation operation skeleton.

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    ./AnnotationOperation.java
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JAL-3878 Fix workers done condition to account for broken jobs.

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JAL-3878 Skip getting results of failed jobs.

JAL-3878 Fix null pointer exception when preparing empty sequences for job.

JAL-3878 Fetch sequences for alignment on menu action, not creation.

JAL-3878 Split web services menu entries by programs and hosts.

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This is waiting for us to define the "language" of edam classifiers that we are going to support. Currently we only define services by what operation they perform but there is plenty of room for fi...

This is waiting for us to define the "language" of edam classifiers that we are going to support. Currently we only define services by what operation they perform but there is plenty of room for fine grained tuning of operations based on other classifiers.

Yes, there are pieces of code that can be reused across multiple if not all other workers. I suppose we can either add component classes that can be used by the workers that need them or we can cre...

Yes, there are pieces of code that can be reused across multiple if not all other workers. I suppose we can either add component classes that can be used by the workers that need them or we can create an abstract base class for all workers with implementations of common methods. The purpose of operation class is to provide metadata and create a worker, so the operation should stay as it is, but the worker needs to be tidied up. I absolutely agree that currently it is too bloated and should be split into smaller pieces but for now I wanted something that just works.
Regarding tuning, the whole point is that now the service is made of operations instead of extending one, so we can create new operations or add extra parameters to the existing operation classes that would alter worker behaviour without touching other parts of the code.