*/
package jalview.datamodel;
-import jalview.analysis.AlignSeq;
-import jalview.util.StringUtils;
-
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
int end;
- Vector pdbIds;
+ Vector<PDBEntry> pdbIds;
String vamsasId;
.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signiature?
+ // Does sequence have the /start-end signature?
if (limitrx.search(name))
{
name = limitrx.left();
{
if (pdbIds == null)
{
- pdbIds = new Vector();
+ pdbIds = new Vector<PDBEntry>();
+ }
+ if (pdbIds.contains(entry))
+ {
+ updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
}
- if (!pdbIds.contains(entry))
+ else
{
pdbIds.addElement(entry);
}
}
+ private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+ {
+ if (newEntry.getFile() != null)
+ {
+ oldEntry.setFile(newEntry.getFile());
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector id)
+ @Override
+ public void setPDBId(Vector<PDBEntry> id)
{
pdbIds = id;
}
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId()
+ @Override
+ public Vector<PDBEntry> getPDBId()
{
return pdbIds;
}
{
if (this.annotation == null)
{
- this.annotation = new Vector();
+ this.annotation = new Vector<AlignmentAnnotation>();
}
if (!this.annotation.contains(annotation))
{