- * <pre>
- * ScoreMatrix displayName
- * # comment lines begin with hash sign
- * # symbol alphabet should be the next non-comment line
- * ARNDCQEGHILKMFPSTWYVBZX *
- * # scores matrix, with space, comma or tab delimited values
- * # [i, j] = score for substituting symbol[i] with symbol[j]
- * # first column in each row is optionally the 'substituted' symbol
- * A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 -4
- * ..etc..
- * </pre>
+ * @return
+ */
+ public int getSize()
+ {
+ return symbols.length;
+ }
+
+ /**
+ * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
+ * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
+ * computed using the current score matrix. For example
+ * <ul>
+ * <li>Sequences:</li>
+ * <li>FKL</li>
+ * <li>R-D</li>
+ * <li>QIA</li>
+ * <li>GWC</li>
+ * <li>Score matrix is BLOSUM62</li>
+ * <li>Gaps treated same as X (unknown)</li>
+ * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
+ * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
+ * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
+ * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
+ * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+ * <li>and so on</li>
+ * </ul>
+ */
+ @Override
+ public MatrixI findSimilarities(AlignmentView seqstrings,
+ SimilarityParamsI options)
+ {
+ char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
+ : gapCharacter;
+ String[] seqs = seqstrings.getSequenceStrings(gapChar);
+ return findSimilarities(seqs, options);
+ }
+
+ /**
+ * Computes pairwise similarities of a set of sequences using the given
+ * parameters