FeatureMapSim BaseLabeler::mergeProteinIdentificationsMaps_(const FeatureMapSimVector & maps)
{
// we do not have any features yet (or at least we ignore them), so simply iterate over the protein
// identifications
std::map<String, ProteinHit> prot_hits;
Size channel_index = 1;
for (FeatureMapSimVector::const_iterator maps_iterator = maps.begin(); maps_iterator != maps.end(); ++maps_iterator)
{
if (maps_iterator->getProteinIdentifications().size() == 0)
continue;
for (std::vector<ProteinHit>::const_iterator protein_hit = (*maps_iterator).getProteinIdentifications()[0].getHits().begin();
protein_hit != (*maps_iterator).getProteinIdentifications()[0].getHits().end();
++protein_hit)
{
if (prot_hits.count((*protein_hit).getSequence())) // we already know this protein -- sum up abundances
{
SimIntensityType new_intensity = prot_hits[(*protein_hit).getSequence()].getMetaValue("intensity");
// remember channel intensity
prot_hits[(*protein_hit).getSequence()].setMetaValue("intensity_" + String(channel_index), new_intensity);
new_intensity += static_cast<SimIntensityType>((*protein_hit).getMetaValue("intensity"));
prot_hits[(*protein_hit).getSequence()].setMetaValue("intensity", new_intensity);
}
else // new protein hit .. remember
{
ProteinHit protHit(*protein_hit);
protHit.setMetaValue("intensity_" + String(channel_index), protHit.getMetaValue("intensity"));
prot_hits.insert(std::pair<String, ProteinHit>((*protein_hit).getSequence(), protHit));
}
}
++channel_index;
}
FeatureMapSim final_map;
ProteinIdentification protIdent;
for (std::map<String, ProteinHit>::iterator prot_hit_iter = prot_hits.begin(); prot_hit_iter != prot_hits.end(); ++prot_hit_iter)
{
protIdent.insertHit(prot_hit_iter->second);
}
std::vector<ProteinIdentification> protIdents;
protIdents.push_back(protIdent);
final_map.setProteinIdentifications(protIdents);
return final_map;
}
void MSSim::createFeatureMap_(const SimTypes::SampleProteins& proteins, SimTypes::FeatureMapSim& feature_map, Size map_index)
{
// clear feature map
feature_map.clear(true);
ProteinIdentification protIdent;
for (SimTypes::SampleProteins::const_iterator it = proteins.begin(); it != proteins.end(); ++it)
{
// add new ProteinHit to ProteinIdentification
ProteinHit protHit(0.0, 1, (it->entry).identifier, (it->entry).sequence);
// copy all meta values from FASTA file parsing
protHit = (it->meta);
// additional meta values:
protHit.setMetaValue("description", it->entry.description);
protHit.setMetaValue("map_index", map_index);
protIdent.insertHit(protHit);
}
vector<ProteinIdentification> vec_protIdent;
vec_protIdent.push_back(protIdent);
feature_map.setProteinIdentifications(vec_protIdent);
}