*/
public void setName(String name);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
+
/**
* Get the display name
*/
* get a range on the sequence as a string
*
* @param start
- * position relative to start of sequence including gaps (from 0)
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
* @param end
- * position relative to start of sequence including gaps (from 0)
+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
*
* @return String containing all gap and symbols in specified range
*/
public int findPosition(int i);
/**
- * Returns the from-to sequence positions (start..) for the given column
- * positions (1..), or null if no residues are included in the range
+ * Returns the sequence positions for first and last residues lying within the
+ * given column positions [fromColum,toColumn] (where columns are numbered
+ * from 1), or null if no residues are included in the range
*
* @param fromColum
+ * - first column base 1. (0 and negative positions are rounded up)
* @param toColumn
- * @return
+ * - last column, base 1
+ * @return null if fromColum>toColumn
*/
- public Range findPositions(int fromColum, int toColumn);
+ public ContiguousI findPositions(int fromColum, int toColumn);
/**
* Returns an int array where indices correspond to each residue in the
public List<DBRefEntry> getPrimaryDBRefs();
/**
+ * Answers true if the sequence has annotation for Hidden Markov Model
+ * information content, else false
+ */
+ boolean hasHMMAnnotation();
+
+ /**
* Returns a (possibly empty) list of sequence features that overlap the given
* alignment column range, optionally restricted to one or more specified
* feature types. If the range is all gaps, then features which enclose it are
* @param c1
* @param c2
*/
- public int replace(char c1, char c2);
+ 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
*/
- public String getSequenceStringFromIterator(Iterator<int[]> it);
+ 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);
+ int firstResidueOutsideIterator(Iterator<int[]> it);
+
+ /**
+ * Answers true if this sequence has an associated Hidden Markov Model
+ *
+ * @return
+ */
+ boolean hasHMMProfile();
}