void DetectabilitySimulation::svmFilter_(SimTypes::FeatureMapSim& features)
{
// transform featuremap to peptides vector
vector<String> peptides_vector(features.size());
for (Size i = 0; i < features.size(); ++i)
{
peptides_vector[i] = features[i].getPeptideIdentifications()[0].getHits()[0].getSequence().toUnmodifiedString();
}
vector<double> labels;
vector<double> detectabilities;
predictDetectabilities(peptides_vector, labels, detectabilities);
// copy all meta data stored in the feature map
SimTypes::FeatureMapSim temp_copy(features);
temp_copy.clear(false);
for (Size i = 0; i < peptides_vector.size(); ++i)
{
if (detectabilities[i] > min_detect_)
{
features[i].setMetaValue("detectability", detectabilities[i]);
temp_copy.push_back(features[i]);
}
#ifdef DEBUG_SIM
cout << detectabilities[i] << " " << min_detect_ << endl;
#endif
}
features.swap(temp_copy);
}
void ITRAQLabeler::labelPeptide_(const Feature& feature, SimTypes::FeatureMapSim& result) const
{
// modify with iTRAQ modification (needed for mass calculation and MS/MS signal)
//site="Y" - low abundance
//site="N-term"
//site="K" - lysine
String modification = (itraq_type_ == ItraqConstants::FOURPLEX ? "iTRAQ4plex" : "iTRAQ8plex");
vector<PeptideHit> pep_hits(feature.getPeptideIdentifications()[0].getHits());
AASequence seq(pep_hits[0].getSequence());
// N-term
seq.setNTerminalModification(modification);
// all "K":
for (Size i = 0; i < seq.size(); ++i)
{
if (seq[i] == 'K' && !seq[i].isModified())
seq.setModification(i, modification);
}
result.resize(1);
result[0] = feature;
pep_hits[0].setSequence(seq);
result[0].getPeptideIdentifications()[0].setHits(pep_hits);
// some "Y":
// for each "Y" create two new features, depending on labeling efficiency on "Y":
if (y_labeling_efficiency_ == 0)
return;
for (Size i = 0; i < seq.size(); ++i)
{
if (seq[i] == 'Y' && !seq[i].isModified())
{
if (y_labeling_efficiency_ == 1)
{
addModificationToPeptideHit_(result.back(), modification, i);
}
else // double number of features:
{
Size f_count = result.size();
for (Size f = 0; f < f_count; ++f)
{
// copy feature
result.push_back(result[f]);
// modify the copy
addModificationToPeptideHit_(result.back(), modification, i);
// adjust intensities:
result.back().setIntensity(result.back().getIntensity() * y_labeling_efficiency_);
result[f].setIntensity(result[f].getIntensity() * (1 - y_labeling_efficiency_));
}
}
}
}
}