public static void test1() {
Sequence[] seqs = Parser.test1();
double[][] distances = (new GappedHammingDistance()).getDistanceMatrix(seqs);
DecimalFormat f = new DecimalFormat("0000.000");
System.out.println(" " + seqs.length);
for (int i = 0; i < seqs.length; i++) {
System.out.print(seqs[i].name);
for (int k = 0; k < 10 - seqs[i].name.length(); k++) {
System.out.print(" ");
}
System.out.print(" ");
int cols = 1;
for (int j = 0; j < seqs.length; j++) {
if (i != j) {
int di = i;
int dj = j;
// force symmetric matrix - arg - what the???
// testing!!!
if (j > i) {
di = j;
dj = i;
}
double d = distances[di][dj];
// testing
if (d > 2000) {
System.err.println("ARGH");
}
System.out.print(f.format(d));
} else {
System.out.print(f.format(0));
}
System.out.print(" ");
cols++;
if (cols >= 7) {
System.out.println();
System.out.print(" ");
cols = 0;
}
}
if (cols != 7) {
System.out.println();
}
}
}
