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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 JPred can now successfully submit and track the job.

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Some preliminary refactoring

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Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work! Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this m...

Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work!
Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this method seems to be trying to do two different things.

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called). So what is it there for?

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called).
So what is it there for?

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Needs proper Javadoc

Needs proper Javadoc

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide...

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide documentation.
e.g. http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=doc/JalviewJS-startupParams.md;h=9ff33529b2dbc2da34d2a573ccf5d042194fbb0d;hb=refs/heads/Jalview-JS/develop

Due to the number of changes this is likely to be a 'best efforts' review.

Due to the number of changes this is likely to be a 'best efforts' review.

Commits to JS-develop from 2nd to 25th June 2020
Commits to JS-develop from 2nd to 25th June 2020
I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

JAL-3446 from JAL-3253 Discoverers

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JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop

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temp push

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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 configure annotation service manager from service’s input validation flags

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JAL-3070 rename AbstractJabaCalcWorker to SeqAnnotationServiceCalcWorker

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    ./JabawsMsaInterfaceAlignCalcWorker.java
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JAL-3070 ensure RNAAliFold annotation rows display correctly

JAL-3070 formatting

JAL-3070 javadoc for (mostly) jabaws specific methods

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

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    ./AAConClient.java
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    ./AADisorderClient.java
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    ./JabawsAnnotationInstance.java
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    ./JabawsMsaInterfaceAlignCalcWorker.java
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    ./JabawsServiceInstance.java
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    ./RNAalifoldClient.java
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JAL-3070 JAL-1379 deferred work on annotation based on JABAWS MSA service (e.g. Jpred3 Jabaws 2.1 deprecated service)

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    ./JabawsMsaInterfaceAlignCalcWorker.java
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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

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