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JAL-3904 failing test

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    ./structures/JalviewStructureDisplayI.java
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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.

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JAL-3863 passing test to verify a uniprot accession with canonical flag set is transferred via the DBRefFetcher (and the SequenceI.transferAnnotation method it calls)

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patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
Merge branch 'features/JAL-2349_matrixvis' into features/JAL-2349_matrixvis_2112

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JAL-3690 Remove references to old AlignCalcManager.

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WIP
WIP
JAL-3690 Introduce AlignCalcManager2 tests.

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JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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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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    ./PollableAlignCalcWorkerI.java
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JAL-3690 - introduce shutdown method that cleans up manager's resources.

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JAL-3690 Documentation for AlignCalcListener

JAL-3690 Catch and notify about worker cancellation separately.

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JAL-3690 Documentation for AlignCalcManagerI2

JAL-3748 store an AlignmentView for the complement within an viewport’s AlignView so it can be recovered after a web service operation

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JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer

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JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer Conflicts: resources/lang/Messages.properties resources/lang/Messages_es.properties

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JAL-3490 merged with 2.11.2 develop

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JAL - 3690 AlignCalc rebuilt - WIP

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    ./AlignCalcListener.java
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    ./AlignCalcManagerI2.java
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JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

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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.

JAL-3390: Option to hide unmapped residues in structure viewer
JAL-3390: Option to hide unmapped residues in structure viewer
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?