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JAL-3692 JAL-3861 remove extra call to .parse() so we don’t process the file again

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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    ./jws2/SequenceAnnotationWSClient.java
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JAL-3878 Remove throws declaration from param store construction.

JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

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JAL-3829 JAL-3855 ignore case when detecting alphafold ID

JAL-3829 3d-beacons doesn’t work as a sequence source just now

Add RNAalifold service instance to slivka web services.

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    ./slivkaws/RNAalifoldServiceInstance.java
JAL-3929 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with retrieval URIs discovered via 3d beacons

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JAL-3829 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with retrieval URIs discovered via 3d beacons

  1. … 2 more files in changeset.
JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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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
remove debugging printlns

remove debugging printlns

aim is normally to avoid creating query-specific data containers on the core query response class

aim is normally to avoid creating query-specific data containers on the core query response class

? not sure this is correct

? not sure this is correct

Needs additionally: model_category created sequence_identity uniprot_start uniprot_end resolution coverage qmean_version ? model_version

Needs additionally:
model_category
created
sequence_identity
uniprot_start
uniprot_end
resolution
coverage
qmean_version ?
model_version

Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
JAL-3855 JAL-2349 (d0h) class for holding and accessing PAE as a contact matrix

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    ./datamodel/alphafold/PAEContactMatrix.java
JAL-3855 EBI Alphafold database fetcher

JAL-3855 JAL-2349 download PAE matrix along with alpha fold structure from EBI and view PAE as contact map

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Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka-integration

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    ./slivkaws/SlivkaJPredServiceInstance.java
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    ./slivkaws/SlivkaMsaServiceInstance.java
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    ./slivkaws/SlivkaWSInstance.java
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Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

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    ./slivkaws/SlivkaWSInstance.java
JAL-3855 ALPHAFOLD database source based on the PDB retriever

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    ./dbsources/EBIAlfaFold.java
JAL-3848 ensure annotation from a service gets a calcId so it can be updated and tracked across multiple views - nb - service.getId() probably isn’t the right value to use for this!

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    ./slivkaws/SlivkaAnnotationServiceInstance.java
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JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script