/**
* A sequence distance score models, that provides a method to compute distances
- * between pairs of sequences
+ * between pairs of sequences. The options parameter provides configuration
+ * choices for how the similarity score is calculated.
*
* @author gmcarstairs
*
* measure
*
* @param seqData
+ * @param options
* @return
*/
- MatrixI findDistances(AlignmentView seqData);
+ MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
}