public static UMatrix createUMatrix(String[] amino, int[][] pam) { UMatrix s = new UMatrix(pam.length); for (int i = 0; i < pam.length; ++i) { for (int j = 0; j <= i; ++j) { AnceWPair max = new AnceWPair(null, Integer.MIN_VALUE); for (int k = 0; k < pam.length; ++k) { AnceWPair temp = new AnceWPair("" + k, pam[k][i] + pam[k][j]); if (max.compare(temp) < 0) max = temp; } max.set_name(amino[Integer.parseInt(max.name())]); s.set_e_at(i, j, max); } } return s; }
public static String prettyPrint(AnceWPair[][] matrix) { return prettyPrint(AnceWPair.ancePart(matrix)) + "\n" + prettyPrint(AnceWPair.wPart(matrix)); }