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));
}
