return anns;
}
+ public boolean updatePDBIds()
+ {
+ if (dbrefs==null || dbrefs.length==0)
+ {
+ return false;
+ }
+ Vector newpdb = new Vector();
+ for (int i=0; i<dbrefs.length;i++)
+ {
+ if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+ {
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setId(dbrefs[i].getAccessionId());
+ if (pdbIds==null || pdbIds.size()==0)
+ {
+ newpdb.addElement(pdbe);
+ } else {
+ Enumeration en = pdbIds.elements();
+ boolean matched=false;
+ while (!matched && en.hasMoreElements())
+ {
+ PDBEntry anentry = (PDBEntry) en.nextElement();
+ if (anentry.getId().equals(pdbe.getId()))
+ {
+ matched=true;
+ }
+ }
+ if (!matched)
+ {
+ newpdb.addElement(pdbe);
+ }
+ }
+ }
+ }
+ if (newpdb.size()>0)
+ {
+ Enumeration en = newpdb.elements();
+ while (en.hasMoreElements())
+ {
+ addPDBId((PDBEntry) en.nextElement());
+ }
+ return true;
+ }
+ return false;
+ }
+
}
public interface SequenceI
{
/**
- * DOCUMENT ME!
+ * Set the display name for the sequence
*
- * @param name DOCUMENT ME!
+ * @param name
*/
public void setName(String name);
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Get the display name
*/
public String getName();
/**
- * DOCUMENT ME!
+ * Set start position of first non-gapped symbol in sequence
*
- * @param start DOCUMENT ME!
+ * @param start new start position
*/
public void setStart(int start);
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * get start position of first non-gapped residue in sequence
+ * @return
*/
public int getStart();
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * get the displayed id of the sequence
+ * @return true means the id will be returned in the form DisplayName/Start-End
*/
public String getDisplayId(boolean jvsuffix);
/**
- * DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
+ * set end position for last residue in sequence
+ * @param end
*/
public void setEnd(int end);
/**
- * DOCUMENT ME!
+ * get end position for last residue in sequence
+ * getEnd()>getStart() unless sequence only consists of gap characters
*
- * @return DOCUMENT ME!
+ * @return
*/
public int getEnd();
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return length of sequence including gaps
+
*/
public int getLength();
/**
- * DOCUMENT ME!
+ * Replace the sequence with the given string
*
- * @param sequence DOCUMENT ME!
+ * @param sequence new sequence string
*/
public void setSequence(String sequence);
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return sequence as string
*/
public String getSequenceAsString();
/**
- * DOCUMENT ME!
- *
+ * get a range on the seuqence as a string
* @param start DOCUMENT ME!
* @param end DOCUMENT ME!
*
public Vector getPDBId();
public void addPDBId(PDBEntry entry);
+ /**
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural databases
+ * @return true if PDBEntry list was modified
+ */
+ public boolean updatePDBIds();
public String getVamsasId();