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); }