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Revert "Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration"

This reverts commit 95f4ae66fbaecbbdc1c3ab3c6c9c611a3a9a3e46, reversing

changes made to bc7c2cf5500c5a4124a69ef8e7b1374d8997558f.

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JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    ./JPredMutlipleAlignmentServiceI.java
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    ./JPredServiceI.java
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JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    ./JPredMutlipleAlignmentServiceI.java
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JAL-3807 - Move new JPred client to the jws2 package.

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JAL-3807 - Move new JPred client to the jws2 package.

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JAL-3807 - Re-implement results processing.

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JAL-3807 - Re-implement results processing.

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This one should be compiling

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Implementing JPredThread methods and SlivkaJPredServiceInstance

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Implementing JPredThread methods and SlivkaJPredServiceInstance

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JAL-3807 JPred can now successfully submit and track the job.

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    ./JPredMutlipleAlignmentServiceI.java
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Some preliminary refactoring

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    ./JPredMutlipleAlignmentServiceI.java
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JAL-3690 patch out need for java.time in j2s (see https://github.com/BobHanson/java2script/issues/194 )

JAL-3070 discoverers return ServiceWithParameter, now containing logic and call code for MsaWSClient or SequenceAnnotationWSClient.attachWSMenuEntry

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JAL-3070 JAL-3066 JAL-3067 refactor annotation web service so client is passed sequences as input, and an alignment object containing result sequences to be annotated.

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JAL-3066 JAL-3070 pull up non-jabaws specific service descriptor components for annotation style web services

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JAL-3070 rename AbstractJabaCalcWorker to SeqAnnotationServiceCalcWorker

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JAL-3070 rough-and-ready refactor of JABA SequenceAnnotation style services - needs some review and refinement

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    ./SequenceAnnotationServiceI.java
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    ./WSAnnotationCalcManagerI.java
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JAL-3066 Implement clustaloWS using slivka system.

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JAL-3070 standard way of storing/recovering documentation URL for service

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JAL-3070 additional interfaces for web services (not yet used!)

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    ./DistanceMatrixResultI.java
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    ./MsaWithGuideTreeI.java
JAL-3070 web service handle with UIinfo.hasParameters() == true => instanceof ServiceWithParameters

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JAL-3070 base interface for service endpoint implementation factory

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    ./JalviewServiceEndpointProviderI.java
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JAL-3070 refactored Client specific code from jalview.ws.jws2.MSA* as implementors of jalview.ws.api.* interfaces

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    ./JalviewWebServiceI.java
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    ./MultipleSequenceAlignmentI.java
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JAL-3070 abstract class for services with adjustable parameters

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    ./ServiceWithParameters.java
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JAL-3070 UIinfo provides JobParameterStoreI

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JAL-3070 pull up hostURL and postURL to UIinfo and getter for action ext

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JAL-3070 core service descriptors for JABAWS services abstracted to jalview.ws.api.UIinfo Note: The jws2.WSClient’s ’serviceType’ is now UIinfo.getName() - reflecting that serviceType was actually the name of the service

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JAL-3070 refactored base analysis action descriptor from RestClient for use in all web service clients

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