import java.awt.Color;
import java.util.List;
+import java.util.Locale;
import java.util.Vector;
public class PDBChain
public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
{
- this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
+ this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(Locale.ROOT);
this.id = theId;
if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
{
* @param seq
* @param status
* The Status of the transferred annotation
- * @param actualGroupId the group id for the features on the destination sequence (e.g. the official accession ID)
+ *
+ * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
*/
public void transferRESNUMFeatures(SequenceI seq,
- String status)
+ String status, String altPDBID)
{
+ if (altPDBID==null)
+ {
+ altPDBID = pdbid;
+ }
SequenceI sq = seq;
while (sq != null && sq.getDatasetSequence() != null)
{
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
- pdbid, feature.getScore());
+ altPDBID, feature.getScore());
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0)
? ""