+ return ss;
+ }
+
+ /**
+ * Retrieve the substitution matrix.
+ *
+ * @return The substitution matrix.
+ */
+ private double[][] getSubstitutionMatrix() {
+ // Defining the substitution matrix
+ // This matrix map distance scores between secondary structure symbols
+
+ return new double[][]{
+ // C E H G
+ {0.0, 1.0, 1.0, 1.0}, // C - COIL
+ {1.0, 0.0, 1.0, 1.0}, // E - SHEET
+ {1.0, 1.0, 0.0, 1.0}, // H - HELIX
+ {1.0, 1.0, 1.0, 0.0} // G - GAP
+
+ };