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JAL-4071 first working prototype

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JAL-4071 boring GUI bits - add togglable menu item for show/hide sequence feature counts and viewModel/viewStyleI methods

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JAL-518 refactored groovy script into main codebase as an Edit Command and alignment view controller method. Left and Right Justify operations now in Edit menu on alignment window and selection popup.

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JAL-4061 use alignment panel’s feature renderer to limit search to just the visible features

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JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequences() to clipboard

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JAL-4061 JAL-4062 Find can now search features

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JAL-4047 - proof of concept for JAL-4048 - display columns of info in sequence ID panel.

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Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

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JAL-3438 spotless for 2.11.2.0

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JAL-3438 - all src and test run through spotless..

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JAL-819 update branch 'feature/JAL-819undeleteAutoannotation' from 2.11.2 develop

Conflicts:

src/jalview/api/AlignViewportI.java

src/jalview/gui/AnnotationLabels.java

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JAL-3878 Add methods to get and remove workers by their calc name.

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JAL-3878 Add methods to get and remove workers by their calc name.

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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-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. … 8 more files in changeset.
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