*/
package jalview.util;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-
public class DBRefUtils
{
private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
{
return false;
}
- String coordsys = dasCoordinateSystemsLookup.get(string
- .toLowerCase());
+ String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
return coordsys == null ? false : coordsys.equals(dBRefEntry
.getSource());
}
{
return null;
}
- String canonical = canonicalSourceNameLookup.get(source
- .toLowerCase());
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
return canonical == null ? source : canonical;
}
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
- if (chaincode==null)
+ if (chaincode == null)
{
chaincode = " ";
}
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setType(PDBEntry.Type.PDB);
pdbr.setProperty(new Hashtable());
- pdbr.getProperty().put("CHAIN", chaincode);
+ pdbr.setChainCode(chaincode);
+ // pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
- } else {
- System.err.println("Malformed PDB DR line:"+acn);
+ }
+ else
+ {
+ System.err.println("Malformed PDB DR line:" + acn);
}
}
else