public char[] getSequence();
/**
- * DOCUMENT ME!
+ * get stretch of sequence characters in an array
*
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
+ * @param start absolute index into getSequence()
+ * @param end exclusive index of last position in segment to be returned.
*
- * @return DOCUMENT ME!
+ * @return char[max(0,end-start)];
*/
public char[] getSequence(int start, int end);
*/
public Vector getPDBId();
+ /**
+ * add entry to the vector of PDBIds, if it isn't in the list already
+ * @param entry
+ */
public void addPDBId(PDBEntry entry);
/**
* update the list of PDBEntrys to include any DBRefEntrys citing structural databases
* @return dataset sequence for this sequence
*/
public SequenceI createDatasetSequence();
+
+ /**
+ * Transfer any database references or annotation from entry
+ * under a sequence mapping.
+ * @param entry
+ * @param mp null or mapping from entry's numbering to local start/end
+ */
+ public void transferAnnotation(SequenceI entry, Mapping mp);
}