+ private SimilarityParamsI similarityParams;
+
+ /**
+ * Constructor given sequence data, score model and score calculation
+ * parameter options.
+ *
+ * @param seqData
+ * @param sqs
+ * @param nuc
+ * @param sm
+ * @param params
+ */
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
+ SimilarityParamsI params)