OpenMS::AASequence getAASequence(const OpenMS::TargetedExperiment::Peptide& peptide)
{
OpenMS::ModificationsDB* mod_db = OpenMS::ModificationsDB::getInstance();
OpenMS::AASequence aas = peptide.sequence;
for (std::vector<OpenMS::TargetedExperiment::Peptide::Modification>::const_iterator it = peptide.mods.begin(); it != peptide.mods.end(); ++it)
{
// Step 1: First look for a cv term that says which unimod nr it is...
// compare with code in source/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.C
int nr_modifications_added = 0;
Map<String, std::vector<CVTerm> > cv_terms = it->getCVTerms();
for (Map<String, std::vector<CVTerm> >::iterator li = cv_terms.begin(); li != cv_terms.end(); ++li)
{
std::vector<CVTerm> mods = (*li).second;
for (std::vector<CVTerm>::iterator mo = mods.begin(); mo != mods.end(); ++mo)
{
// if we find a CV term that starts with UniMod, chances are we can use the UniMod accession number
if (mo->getAccession().size() > 7 && mo->getAccession().prefix(7).toLower() == String("unimod:"))
{
nr_modifications_added++;
setModification(it->location, boost::numeric_cast<int>(peptide.sequence.size()), "UniMod:" + mo->getAccession().substr(7), aas);
}
}
}
// Step 2: If the above step fails, try to find the correct
// modification some other way, i.e. by using the mass difference
if (nr_modifications_added == 0)
{
std::vector<String> mods;
mod_db->getModificationsByDiffMonoMass(mods, peptide.sequence[it->location], it->mono_mass_delta, 0.0);
for (std::vector<String>::iterator mo = mods.begin(); mo != mods.end(); ++mo)
{
nr_modifications_added++;
setModification(it->location, boost::numeric_cast<int>(peptide.sequence.size()), *mo, aas);
}
}
// In theory, each modification in the TraML should map to one modification added to the AASequence
if (nr_modifications_added > 1)
{
std::cout << "Warning: More than one modification was found for peptide " << peptide.sequence << " at position " << it->location << std::endl;
}
else if (nr_modifications_added == 0)
{
std::cout << "Warning: Could not determine modification with delta mass " << it->mono_mass_delta << " for peptide " << peptide.sequence << " at position " << it->location << std::endl;
}
}
return aas;
}
ModificationDefinition::ModificationDefinition(const String & mod) :
term_spec_(ResidueModification::ANYWHERE),
mod_(0),
fixed_modification_(true),
max_occurences_(0)
{
setModification(mod);
}
void UVManager::ajouterUV(const QString& c, const QString& t, QMap<QString,int> cat, bool a, bool p){
if (trouverUV(c)) {
throw UTProfilerException(QString("erreur, UVManager, UV ")+c+QString("déja existante"));
}else{
UV* newuv=new UV(c,t,cat,a,p);
addItem(newuv);
setModification();
}
}
