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JAL-3878 Add getCalcName to AlignCalcWorkerI.

getCalcName() can be used to identify services that run the calculator.

when an alternative calculator (different host or parameters) is created

the old ones sharing the name can be stopped.

  1. … 3 more files in changeset.
JAL-3690 Remove references to old AlignCalcManager.

  1. … 4 more files in changeset.
WIP
WIP
JAL-3690 Introduce AlignCalcManager2 tests.

  1. … 2 more files in changeset.
JAL-3690 AlignCalcManager - add full support for oneshot workers

JAL-3690 AlignCalcManager - add full support for oneshot workers

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Allow unregistered workers to be run with CalcManager.

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

  1. … 56 more files in changeset.
JAL-3690 List.copyOf() workaround

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

  1. … 9 more files in changeset.
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)

  1. … 2 more files in changeset.
JAL-3690 - introduce shutdown method that cleans up manager's resources.

  1. … 3 more files in changeset.
JAL-3690 Catch and notify about worker cancellation separately.

  1. … 1 more file in changeset.
JAL-3690 Fix concurrent modification exception when workers are cancelled

JAL - 3690 AlignCalc rebuilt - WIP

    • -0
    • +321
    ./AlignCalcManager2.java
  1. … 8 more files in changeset.
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

  1. … 11 more files in changeset.
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

  1. … 11 more files in changeset.
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