import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Set;
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
pdbr.setType(PDBEntry.Type.PDB);
- pdbr.setProperty(new Hashtable());
pdbr.setChainCode(chaincode);
- // pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
}
else
* sequences if they have an appropriate primary ref
* <table>
* <tr>
- * <td>Seq Type</td>
- * <td>Primary DB</td>
- * <td>Direct which will be promoted</td>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
* </tr>
- * <tr>
+ * <tr align=center>
* <td>peptides</td>
* <td>Ensembl</td>
* <td>Uniprot</td>
* </tr>
- * <tr>
+ * <tr align=center>
* <td>peptides</td>
* <td>Ensembl</td>
* <td>Uniprot</td>
* </tr>
- * <tr>
+ * <tr align=center>
* <td>dna</td>
* <td>Ensembl</td>
* <td>ENA</td>
return;
}
List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
- selfs.addAll(Arrays.asList(selectDbRefs(!sequence.isProtein(),
- sequence.getDBRefs())));
+ {
+ DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+ sequence.getDBRefs());
+ if (selfArray == null || selfArray.length == 0)
+ {
+ // nothing to do
+ return;
+ }
+ selfs.addAll(Arrays.asList(selfArray));
+ }
// filter non-primary refs
for (DBRefEntry p : pr)