- /*
- * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
- * for pairwise scoring; 2.10.2 uses gap score (last column) in
- * score matrix (JAL-2397)
- * Set this flag to true (via Groovy) for 2.10.1 behaviour
- */
- private static boolean scoreGapAsAny = false;
-
- public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
- boolean nucleotide2)
- {
- seqstrings = seqstrings2;
- seqs = seqs2;
- nucleotide = nucleotide2;
- score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
- }
-