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; }