Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

    • -1
    • +3
    ./jabaws/DisorderAnnotExportImport.java
  1. … 99 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)

  1. … 3 more files in changeset.
JAL-3863 fix test and note about fragility

JAL-3863 fix test and note about fragility

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

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

  1. … 2 more files in changeset.
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
JAL-3855 JAL-2349 download PAE matrix along with alpha fold structure from EBI and view PAE as contact map

  1. … 1 more file in changeset.
JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws

    • -3
    • +18
    ./jabaws/DisorderAnnotExportImport.java
WIP
WIP
JAL-3725 exclude stop codon from CDS-to-protein mapping

    • -11
    • +12
    ./dbsources/EmblXmlSourceTest.java
  1. … 1 more file in changeset.
JAL-3725 exclude stop codon from CDS-to-protein mapping

  1. … 1 more file in changeset.
JAL-3725 exclude stop codon from CDS-to-protein mapping

    • -11
    • +12
    ./dbsources/EmblXmlSourceTest.java
  1. … 1 more file in changeset.
JAL-3692 unit test updated for ?gzip download endpoint URL

JAL-3692 unit test updated for ?gzip download endpoint URL

JAL-3692 unit test updated for ?gzip download endpoint URL

changed

changed

Should be ENA Flatfile retrieval failed

Should be ENA Flatfile retrieval failed

JAL-3692: Update ENA endpoint for EMBL/CDS sequence retrieval
JAL-3692: Update ENA endpoint for EMBL/CDS sequence retrieval
JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

JAL-3692 URL tests updated

JAL-3692 URL tests updated

JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)

    • -0
    • +498
    ./dbsources/EmblXmlSourceTest.java
  1. … 10 more files in changeset.
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings) Conflicts: src/jalview/ws/dbsources/EmblXmlSource.java src/jalview/ws/ebi/EBIFetchClient.java

    • -0
    • +498
    ./dbsources/EmblXmlSourceTest.java
  1. … 10 more files in changeset.