+ /*
+ * verify that with a symmetric score matrix,
+ * pairwise similarity matrix is also symmetric
+ * seq1.seq1 = 5*A.A + 3*B.B = 5+9 = 14
+ * seq1.seq2 = 3*A.A + 2*A.B + B.A + 2*B.B = 3 + -4 + -2 + 6 = 3
+ * seq2.seq1 = 3*A.A + A.B + 2*B.A + 2*B.B = 3 + -2 + -4 + 6 = 3
+ * seq2.seq2 = 4*A.A + 4*B.B = 4 + 12 = 16
+ */
+ SimilarityParamsI params = new SimilarityParams(true, true, true,
+ false);
+ String seq1 = "AAABBBAA";
+ String seq2 = "AABBABBA";
+ String[] seqs1 = new String[] { seq1, seq2 };
+ MatrixI res1 = sm.findSimilarities(seqs1, params);
+ assertEquals(res1,
+ new Matrix(new double[][]
+ { { 14d, 3d }, { 3d, 16d } }));
+
+ /*
+ * order of sequences affects diagonal, but not off-diagonal values
+ * [0, 0] is now seq2.seq2, [1, 1] is seq1.seq1
+ * [0, 1] is now seq2.seq1 = seq1.seq2 by symmetry
+ */
+ String[] seqs2 = new String[] { seq2, seq1 };
+ MatrixI res2 = sm.findSimilarities(seqs2, params);
+ assertFalse(res1.equals(res2));
+ assertEquals(res2,
+ new Matrix(new double[][]
+ { { 16d, 3d }, { 3d, 14d } }));
+
+ /*
+ * now make the score matrix asymmetric
+ * seq1.seq1 = 5*A.A + 3*B.B = 5+9 = 14
+ * seq1.seq2 = 3*A.A + 2*A.B + B.A + 2*B.B = 3 + -4 + 2 + 6 = 7
+ * seq2.seq1 = 3*A.A + A.B + 2*B.A + 2*B.B = 3 + -2 + 4 + 6 = 11
+ * seq2.seq2 = 4*A.A + 4*B.B = 4 + 12 = 16
+ */
+ scores = new float[][] { { 1f, -2f }, { 2f, 3f } };