public HiddenMarkovModel getHMM();
public void setHMM(HiddenMarkovModel hmm);
-
/**
* Get the display name
*/
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
-
/**
* Answers true if the sequence has annotation for Hidden Markov Model
* information content, else false
* @param c1
* @param c2
*/
- int replace(char c1, char c2);
+ public int replace(char c1, char c2);
/**
* Answers the GeneLociI, or null if not known
* the iterator to use
* @return a String corresponding to the sequence
*/
- String getSequenceStringFromIterator(Iterator<int[]> it);
+ public String getSequenceStringFromIterator(Iterator<int[]> it);
/**
* Locate the first position in this sequence which is not contained in an
* iterator over regions
* @return first residue not contained in regions
*/
-
public int firstResidueOutsideIterator(Iterator<int[]> it);