protected void addToCentroid(Matrix m, PositionWeightMatrix pwm) {
for (int i = 0; i < m.getColumnDimension(); i++) {
PositionWeightColumn c = pwm.get(i);
for (int j = 0; j < m.getRowDimension(); j++) {
m.set(j, i, m.get(j, i) + c.getWeight(j));
}
}
}
public void write(BufferedWriter bw, NumberFormat formatter) throws IOException {
bw.write(">" + name);
bw.newLine();
if (size() > 0) {
int rows = get(0).getAlphabetSize();
for (int i = 0; i < rows; i++) {
Iterator<PositionWeightColumn> colIt = iterator();
while (colIt.hasNext()) {
PositionWeightColumn col = colIt.next();
bw.write(formatter.format(col.getWeight(i)));
if (colIt.hasNext()) {
bw.write("\t");
}
}
bw.newLine();
}
}
}