/**
@brief Similarity pairwise score
This function return the similarity score of two spectra based on SteinScott.
@param s1 const PeakSpectrum Spectrum 1
@param s2 const PeakSpectrum Spectrum 2
@see SteinScottImproveScore()
*/
double SteinScottImproveScore::operator()(const PeakSpectrum & s1, const PeakSpectrum & s2) const
{
const double epsilon = (double)param_.getValue("tolerance");
const double constant = epsilon / 10000;
//const double c(0.0004);
double score(0), sum(0), sum1(0), sum2(0), sum3(0), sum4(0);
/* std::cout << s1 << std::endl;
std::cout << std::endl;
std::cout << s2 << std::endl;*/
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
double temp = it1->getIntensity();
sum1 += temp * temp;
sum3 += temp;
}
for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
{
double temp = it1->getIntensity();
sum2 += temp * temp;
sum4 += temp;
}
double z = constant * (sum3 * sum4);
Size j_left(0);
for (Size i = 0; i != s1.size(); ++i)
{
for (Size j = j_left; j != s2.size(); ++j)
{
double pos1(s1[i].getMZ()), pos2(s2[j].getMZ());
if (std::abs(pos1 - pos2) <= 2 * epsilon)
{
sum += s1[i].getIntensity() * s2[j].getIntensity();
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
j_left = j;
}
}
}
}
//std::cout<< sum << " Sum " << z << " z " << std::endl;
score = (sum - z) / (std::sqrt((sum1 * sum2)));
// std::cout<<score<< " score" << std::endl;
if (score < (float)param_.getValue("threshold"))
{
score = 0;
}
return score;
}
double ZhangSimilarityScore::operator()(const PeakSpectrum & s1, const PeakSpectrum & s2) const
{
const double tolerance = (double)param_.getValue("tolerance");
bool use_linear_factor = param_.getValue("use_linear_factor").toBool();
bool use_gaussian_factor = param_.getValue("use_gaussian_factor").toBool();
double score(0), sum(0), sum1(0), sum2(0) /*, squared_sum1(0), squared_sum2(0)*/;
// TODO remove parameter
if (param_.getValue("is_relative_tolerance").toBool() )
{
throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
}
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
sum1 += it1->getIntensity();
/*
for (PeakSpectrum::ConstIterator it2 = s1.begin(); it2 != s1.end(); ++it2)
{
if (abs(it1->getPosition()[0] - it2->getPosition()[0]) <= 2 * tolerance)
{
squared_sum1 += it1->getIntensity() * it2->getIntensity();
}
}*/
}
/*
UInt i_left(0);
for (Size i = 0; i != s1.size(); ++i)
{
sum1 += s1[i].getIntensity();
for (Size j = i_left; j != s1.size(); ++j)
{
double pos1(s1[i].getPosition()[0]), pos2(s1[j].getPosition()[0]);
if (abs(pos1 - pos2) <= 2 * tolerance)
{
squared_sum1 += s1[i].getIntensity() * s1[j].getIntensity();
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
i_left = i;
}
}
}
}*/
/*
i_left = 0;
for (Size i = 0; i != s2.size(); ++i)
{
sum2 += s2[i].getIntensity();
for (Size j = i_left; j != s2.size(); ++j)
{
double pos1(s2[i].getPosition()[0]), pos2(s2[j].getPosition()[0]);
if (abs(pos1 - pos2) <= 2 * tolerance)
{
squared_sum1 += s2[i].getIntensity() * s2[j].getIntensity();
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
i_left = i;
}
}
}
}*/
for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
{
sum2 += it1->getIntensity();
/*
for (PeakSpectrum::ConstIterator it2 = s2.begin(); it2 != s2.end(); ++it2)
{
if (abs(it1->getPosition()[0] - it2->getPosition()[0]) <= 2 * tolerance)
{
squared_sum2 += it1->getIntensity() * it2->getIntensity();
}
}
*/
}
Size j_left(0);
for (Size i = 0; i != s1.size(); ++i)
{
for (Size j = j_left; j != s2.size(); ++j)
{
double pos1(s1[i].getMZ()), pos2(s2[j].getMZ());
if (fabs(pos1 - pos2) < tolerance)
{
//double factor((tolerance - fabs(pos1 - pos2)) / tolerance);
double factor = 1.0;
if (use_linear_factor || use_gaussian_factor)
{
factor = getFactor_(tolerance, fabs(pos1 - pos2), use_gaussian_factor);
}
sum += sqrt(s1[i].getIntensity() * s2[j].getIntensity() * factor);
}
else
{
if (pos2 > pos1)
{
break;
}
else
{
j_left = j;
}
}
}
}
/*
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
for (PeakSpectrum::ConstIterator it2 = s2.begin(); it2 != s2.end(); ++it2)
{
if (abs(it1->getPosition()[0] - it2->getPosition()[0]) <= 2 * tolerance)
{
sum += sqrt(it1->getIntensity() * it2->getIntensity());
}
}
}*/
score = sum / (sqrt(sum1 * sum2));
return score;
}
