public HiddenMarkovModel getHMM();
public void setHMM(HiddenMarkovModel hmm);
-
/**
* Get the display name
*/
String label);
/**
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source), label (type) and description (observation instance).
+ * Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ * @param description
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description);
+ /**
* 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. It will also make a duplicate
* 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);