Method readRTMZCharge_

src/openms/source/FORMAT/PepXMLFile.cpp:923–962

  }

  void PepXMLFile::readRTMZCharge_(const xercesc::Attributes& attributes)
  {
    double mass = attributeAsDouble_(attributes, "precursor_neutral_mass");
    charge_ = attributeAsInt_(attributes, "assumed_charge");
    mz_ = (mass + hydrogen_mass_ * charge_) / charge_;
    rt_ = 0;
    // assume only one scan, i.e. ignore "end_scan":
    // "start and end_scan" are 1-based. "index" is 0-based
    scannr_ = attributeAsInt_(attributes, "start_scan");
    Size endscan = attributeAsInt_(attributes, "start_scan");
    if (scannr_ != endscan)
    {
      error(LOAD, "endscan not equal to startscan. Merged spectrum queries not supported. Parsing start scan nr. only.");
    }

    bool rt_present = optionalAttributeAsDouble_(rt_, attributes, "retention_time_sec");

    if (!rt_present) // get RT from experiment
    {
      if (lookup_ == nullptr || lookup_->empty())
      {
        // no lookup given, report non-fatal error
        error(LOAD, "Cannot get RT information - no spectra given");
        return;
      }

      Size index = (scannr_ != 0) ? lookup_->findByScanNumber(scannr_) :
        lookup_->findByReference(attributeAsString_(attributes, "spectrum"));
      SpectrumMetaDataLookup::SpectrumMetaData meta;
      lookup_->getSpectrumMetaData(index, meta);
      if (meta.ms_level == 2)
      {
        rt_ = meta.rt;
      }
      else
      {
        error(LOAD, "Cannot get RT information - scan mapping is incorrect");
      }
    }
  }

  void PepXMLFile::setParseUnknownScores(bool parse_unknown_scores)
  {