public int findIndex(int pos);
/**
- * Returns the sequence position for an alignment position
+ * Returns the sequence position for an alignment position.
*
* @param i
* column index in alignment (from 0..<length)
*
- * @return residue number for residue (left of and) nearest ith column
+ * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+ * ith column
*/
public int findPosition(int i);
*/
public void addDBRef(DBRefEntry entry);
- public void addSequenceFeature(SequenceFeature sf);
+ /**
+ * Adds the given sequence feature and returns true, or returns false if it is
+ * already present on the sequence
+ *
+ * @param sf
+ * @return
+ */
+ public boolean addSequenceFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
*/
public PDBEntry getPDBEntry(String pdbId);
-
/**
* Get all primary database/accessions for this sequence's data. These
* DBRefEntry are expected to resolve to a valid record in the associated