double AbsoluteQuantitation::calculateRatio(const Feature & component_1, const Feature & component_2, const String & feature_name)
{
double ratio = 0.0;
if (component_1.metaValueExists(feature_name) && component_2.metaValueExists(feature_name))
{
double feature_1 = component_1.getMetaValue(feature_name);
double feature_2 = component_2.getMetaValue(feature_name);
// std::cout << "ratio = " << ratio << "." << std::endl;
ratio = feature_1/feature_2;
}
else if (component_1.metaValueExists(feature_name))
{
LOG_INFO << "Warning: no IS found for component " << component_1.getMetaValue("native_id") << ".";
// std::cout << "Warning: no IS found for component " << component_1.getMetaValue("native_id") << "." << std::endl;
double feature_1 = component_1.getMetaValue(feature_name);
ratio = feature_1;
}
else
{
LOG_INFO << "Feature metaValue " << feature_name << " not found for components " << component_1.getMetaValue("native_id") << " and " << component_2.getMetaValue("native_id") << ".";
// std::cout << "Feature metaValue " << feature_name << " not found for components " << component_1.getMetaValue("native_id") << " and " << component_2.getMetaValue("native_id") << "." << std::endl;
}
return ratio;
}
EigenMatrixXdPtr ITRAQLabeler::getItraqIntensity_(const Feature& f, const double MS2_RT_time) const
{
double factor = getRTProfileIntensity_(f, MS2_RT_time);
//std::cerr << "\n\nfactor is: " << factor << "\n";
// fill map with values present (all missing ones remain 0)
MutableEigenMatrixXdPtr m(new Eigen::MatrixXd(ItraqConstants::CHANNEL_COUNT[itraq_type_], 1));
m->setZero();
Size ch(0);
Size ch_internal(0);
for (ChannelMapType::ConstIterator it = channel_map_.begin(); it != channel_map_.end(); ++it)
{
SimTypes::SimIntensityType intensity(0);
if (it->second.active && f.metaValueExists(getChannelIntensityName(ch_internal))) // peptide is present in this channel
{
intensity = (double) f.getMetaValue(getChannelIntensityName(ch_internal));
++ch_internal;
}
(* m)(ch, 0) = intensity * factor;
++ch;
}
return m;
}
double AbsoluteQuantitation::calculateRatio(const Feature & component_1, const Feature & component_2, const String & feature_name)
{
double ratio = 0.0;
// member feature_name access
if (feature_name == "intensity")
{
if (component_1.metaValueExists("native_id") && component_2.metaValueExists("native_id"))
{
const double feature_1 = component_1.getIntensity();
const double feature_2 = component_2.getIntensity();
ratio = feature_1 / feature_2;
}
else if (component_1.metaValueExists("native_id"))
{
LOG_DEBUG << "Warning: no IS found for component " << component_1.getMetaValue("native_id") << ".";
const double feature_1 = component_1.getIntensity();
ratio = feature_1;
}
}
// metaValue feature_name access
else
{
if (component_1.metaValueExists(feature_name) && component_2.metaValueExists(feature_name))
{
const double feature_1 = component_1.getMetaValue(feature_name);
const double feature_2 = component_2.getMetaValue(feature_name);
ratio = feature_1/feature_2;
}
else if (component_1.metaValueExists(feature_name))
{
LOG_DEBUG << "Warning: no IS found for component " << component_1.getMetaValue("native_id") << ".";
const double feature_1 = component_1.getMetaValue(feature_name);
ratio = feature_1;
}
else
{
LOG_DEBUG << "Feature metaValue " << feature_name << " not found for components " << component_1.getMetaValue("native_id") << " and " << component_2.getMetaValue("native_id") << ".";
}
}
return ratio;
}
