if (prseq != null && prname != null && prid != null)
{
// extract proteins.
- product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
- +((prname.length()==0) ? "" : " " + prname), prseq, prstart, prstart
+ product = new Sequence(prid
+ , prseq, prstart, prstart
+ prseq.length() - 1);
- product.setDescription("Protein Product from " + sourceDb);
+ product.setDescription(((prname.length()==0) ? "Protein Product from " + sourceDb : prname));
if (!noPeptide)
{
{
// TODO: Add a DbRef back to the parent EMBL sequence with the exon
// map
-
+ // if given a dataset reference, search dataset for parent EMBL sequence if it exists and set its map
// make a new feature annotating the coding contig
}
else
if (map!=null && map.getTo()!=null)
{
map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
+ if (map.getTo().getName().indexOf(prid)==0)
+ {
+ map.getTo().setName(jalview.datamodel.DBRefSource.UNIPROT+"|"+ref.getAccessionId());
+ }
}
}
if (product != null)