import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.UniprotFile;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import java.io.InputStream;
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
- ArrayList<DBRefEntry> dbRefs = new ArrayList<DBRefEntry>();
+ ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
dbRefs.add(dbRef);
}
- Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+ Vector<PDBEntry> onlyPdbEntries = new Vector<>();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
}
}
-
}
sequence.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
- for (SequenceFeature sf : entry.getFeature())
+ for (UniprotFeature uf : entry.getFeature())
{
- sf.setFeatureGroup("Uniprot");
- sequence.addSequenceFeature(sf);
+ SequenceFeature copy = new SequenceFeature(uf.getType(),
+ uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+ copy.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(copy);
}
}
for (DBRefEntry dbr : dbRefs)
/**
*
* @param entry
- * UniportEntry
+ * UniprotEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
- // name.append("UniProt/Swiss-Prot");
- // use 'canonicalised' name for optimal id matching
- name.append(DBRefSource.UNIPROT);
- for (String accessionId : entry.getAccession())
- {
- name.append(BAR_DELIMITER);
- name.append(accessionId);
- }
for (String n : entry.getName())
{
- name.append(BAR_DELIMITER);
+ if (name.length() > 0)
+ {
+ name.append(BAR_DELIMITER);
+ }
name.append(n);
}
return name.toString();