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;
}
double ITRAQLabeler::getRTProfileIntensity_(const Feature& f, const double MS2_RT_time) const
{
// compute intensity correction factor for feature from RT profile
const DoubleList& elution_bounds = f.getMetaValue("elution_profile_bounds");
const DoubleList& elution_ints = f.getMetaValue("elution_profile_intensities");
// check that RT is within the elution bound:
OPENMS_POSTCONDITION(f.getConvexHull().getBoundingBox().encloses(MS2_RT_time, f.getMZ()), "The MS2 spectrum has wrong parent features! The feature does not touch the spectrum's RT!")
if (MS2_RT_time < elution_bounds[1] || elution_bounds[3] < MS2_RT_time)
{
LOG_WARN << "Warn: requesting MS2 RT for " << MS2_RT_time << ", but bounds are only from [" << elution_bounds[1] << "," << elution_bounds[3] << "]\n";
return 0;
}
// do linear interpolation
double width = elution_bounds[3] - elution_bounds[1];
double offset = MS2_RT_time - elution_bounds[1];
Int index = floor(offset / (width / (elution_ints.size() - 1)) + 0.5);
OPENMS_POSTCONDITION(index < (Int)elution_ints.size(), "Wrong index computation! (Too large)")
return elution_ints[index];
}
p.setConvexHulls(hulls);
p.getConvexHull(); //this pre-calculates the overall convex hull
Feature::PositionType pos2;
Feature::IntensityType i2;
Feature copy_of_p(p);
i2 = copy_of_p.getIntensity();
pos2 = copy_of_p.getPosition();
TEST_REAL_SIMILAR(i2, 123.456)
TEST_REAL_SIMILAR(pos2[0], 21.21)
TEST_REAL_SIMILAR(pos2[1], 22.22)
TEST_EQUAL(p.getMetaValue("cluster_id"),DataValue(4711));
Feature::QualityType q2;
q2 = copy_of_p.getOverallQuality();
TEST_REAL_SIMILAR(q2, 0.9)
q2 = copy_of_p.getQuality(0);
TEST_REAL_SIMILAR(q2, 0.1)
q2 = copy_of_p.getQuality(1);
TEST_REAL_SIMILAR(q2, 0.2)
TEST_EQUAL(copy_of_p.getConvexHull().getHullPoints().size(),p.getConvexHull().getHullPoints().size())
TEST_EQUAL(copy_of_p.getConvexHulls().size(),p.getConvexHulls().size())
END_SECTION
START_SECTION((Feature& operator = (const Feature& rhs)))
Feature::PositionType pos;
pos[0] = 21.21;
