/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequenceI;
import jalview.datamodel.UniprotEntry;
import jalview.datamodel.UniprotFile;
-import jalview.util.DBRefUtils;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
* UniprotEntry
* @return SequenceI instance created from the UniprotEntry instance
*/
- public SequenceI uniprotEntryToSequenceI(UniprotEntry entry){
+ public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+ {
String id = getUniprotEntryId(entry);
SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
.getContent());
.get("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
- dbr = new DBRefEntry(DBRefSource.EMBLCDS, DBRefSource.UNIPROT
- + ":"
- + dbVersion, cdsId.trim());
+ // remove version
+ String[] vrs = cdsId.split("\\.");
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
dbRefs.add(dbr);
}
}
- if (false) // "Ensembl".equals(pdb.getType()))
+ if ("Ensembl".equals(pdb.getType()))
{
/*UniprotXML
* <dbReference type="Ensembl" id="ENST00000321556">
.get("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
- // Only add the product ID
- dbRefs.remove(dbr);
dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
+ ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
sequence.addSequenceFeature(sf);
}
}
- // we use setDBRefs to assign refs quickly.
- sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
- // need to use ensurePrimaries to reify any refs that should become primary
- // refs
- DBRefUtils.ensurePrimaries(sequence); // promote any direct refs to primary
- // source dbs
+ for (DBRefEntry dbr : dbRefs)
+ {
+ sequence.addDBRef(dbr);
+ }
return sequence;
}