* 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());
if ("EMBL".equals(pdb.getType()))
{
// look for a CDS reference and add it, too.
- String cdsId = (String) pdb.getProperty()
- .get("protein sequence ID");
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
// remove version
dbRefs.add(dbr);
}
}
- if (false) // "Ensembl".equals(pdb.getType()))
+ if ("Ensembl".equals(pdb.getType()))
{
/*UniprotXML
* <dbReference type="Ensembl" id="ENST00000321556">
* <property type="gene ID" value="ENSG00000158828"/>
* </dbReference>
*/
- String cdsId = (String) pdb.getProperty()
- .get("protein sequence ID");
+ String cdsId = (String) pdb.getProperty("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;
}