+ private SimilarityParamsI similarityParams;
+
+ /**
+ * Constructor given sequence data and score calculation parameter options.
+ * The initial state is to compute PCA using a default score model (BLOSUM62
+ * for peptide, DNA for nucleotide).
+ *
+ * @param seqData
+ * @param sqs
+ * @param nuc
+ * @param params
+ */
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ SimilarityParamsI params)