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;
}
Document* PFMatrixFormat::loadDocument( IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& fs, U2OpStatus& os ){
DbiOperationsBlock opBlock(dbiRef, os);
CHECK_OP(os, NULL);
Q_UNUSED(opBlock);
QList<GObject*> objs;
IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(io->getAdapterId());
TaskStateInfo siPFM;
PFMatrix m = WeightMatrixIO::readPFMatrix(iof, io->getURL().getURLString(), siPFM);
if (siPFM.hasError()) {
os.setError(tr("The file format is not PFM"));
} else {
if (m.getLength() == 0) {
os.setError(tr("Zero length or corrupted model\nMaybe model data are not enough for selected algorithm"));
}
}
CHECK_OP(os, NULL);
PFMatrixObject *mObj = PFMatrixObject::createInstance(m, QFileInfo(io->getURL().getURLString()).baseName(), dbiRef, os, fs);
CHECK_OP(os, NULL);
objs.append(mObj);
return new Document(this, io->getFactory(), io->getURL(), dbiRef, objs, fs);
}