public int[] gapMap();
/**
- * DOCUMENT ME!
+ * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
+ * and adjusting start and end positions accordingly.
*
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
+ * @param i first column in range to delete
+ * @param j last column in range to delete
*/
public void deleteChars(int i, int j);
public DBRefEntry[] getDBRef();
+ /**
+ * add the given entry to the list of DBRefs for this sequence,
+ * or replace a similar one if entry contains a map object
+ * and the existing one doesnt.
+ * @param entry
+ */
public void addDBRef(DBRefEntry entry);
public void addSequenceFeature(SequenceFeature sf);
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
+
/**
* Derive a sequence (using this one's dataset or as the dataset)
* @return duplicate sequence with valid dataset sequence
*/
public SequenceI deriveSequence();
+ /**
+ * set the array of associated AlignmentAnnotation for this sequenceI
+ * @param revealed
+ */
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+ /**
+ * Get one or more alignment annotations with a particular label.
+ * @param label string which each returned annotation must have as a label.
+ * @return null or array of annotations.
+ */
+ public AlignmentAnnotation[] getAnnotation(String label);
+ /**
+ * create a new dataset sequence (if necessary)
+ * for this sequence and sets this sequence to refer to it.
+ * This call will move any features or references on the sequence onto the dataset.
+ * @return dataset sequence for this sequence
+ */
+ public SequenceI createDatasetSequence();
}