PWMatrix PWMConversionAlgorithmNLG::convert(const PFMatrix& matrix) {
int size = (matrix.getType() == PFM_MONONUCLEOTIDE) ? 4 : 16;
int sum[16];
memset(sum, 0, size*sizeof(int));
int all_hits = 0;
for (int i = 0; i < size; i++) {
for (int j = 0, n = matrix.getLength(); j < n; j++) {
sum[i] += matrix.getValue(i, j);
all_hits += matrix.getValue(i, j);
}
}
if (all_hits <= 0) {
return PWMatrix();
}
float p[16];
for (int i = 0; i < size; i++) {
p[i] = sum[i];
p[i] /= all_hits;
if (qAbs(p[i]) <= 1e-9) {
return PWMatrix();
}
}
QVarLengthArray<float> res(size*matrix.getLength());
for (int i = 0; i < size; i++) {
for (int j = 0, n = matrix.getLength(); j < n; j++) {
res[matrix.index(i, j)] = -matrix.getValue(i, j)*log(p[i]);
}
}
PWMatrix w(res, (matrix.getType() == PFM_MONONUCLEOTIDE) ? PWM_MONONUCLEOTIDE : PWM_DINUCLEOTIDE);
w.setInfo(UniprobeInfo(matrix.getProperties()));
return w;
}
