Details
Major Description
A standard exercise in Jalview is to demonstrate the display of linked viewing/analysis of protein sequences for
nucleotide sequence contigs containing coding regions. The example accession, V00488 is correctly retrieved, appears to have coding regions (highlighted as features), but no Uniprot cross-references appear in the 'Calculate->Show Cross References' submenu. For other entries, although Uniprot cross references appear. selecting them from the sub-menu results in Jalview retrieving them via web-service rather than showing the protein product shipped with the EMBLXML.
This bug needs to be verified in 2.8.1 and earlier - and tests need to be created, since I seem to remember it has worked in the past, but it is possible that updates to the EMBL XML schema have broken Jalview's code (I note that ENA is now used as a cross-reference, and it's highly likely that Jalview isn't treating ENA cross-references as EMBL cross-references).
nucleotide sequence contigs containing coding regions. The example accession, V00488 is correctly retrieved, appears to have coding regions (highlighted as features), but no Uniprot cross-references appear in the 'Calculate->Show Cross References' submenu. For other entries, although Uniprot cross references appear. selecting them from the sub-menu results in Jalview retrieving them via web-service rather than showing the protein product shipped with the EMBLXML.
This bug needs to be verified in 2.8.1 and earlier - and tests need to be created, since I seem to remember it has worked in the past, but it is possible that updates to the EMBL XML schema have broken Jalview's code (I note that ENA is now used as a cross-reference, and it's highly likely that Jalview isn't treating ENA cross-references as EMBL cross-references).