ExitCodes main_(int, const char**)
  {
    // parsing parameters
    String in(getStringOption_("in"));
    String feature_in(getStringOption_("feature_in"));
    String out(getStringOption_("out"));
    double precursor_mass_tolerance(getDoubleOption_("precursor_mass_tolerance"));

    // reading input
    FileHandler fh;
    FileTypes::Type in_type = fh.getType(in);

    PeakMap exp;
    fh.loadExperiment(in, exp, in_type, log_type_, false, false);
    exp.sortSpectra();

    FeatureMap feature_map;
    if (feature_in != "")
    {
      FeatureXMLFile().load(feature_in, feature_map);
    }

    // calculations
    FeatureFinderAlgorithmIsotopeWavelet iso_ff;
    Param ff_param(iso_ff.getParameters());
    ff_param.setValue("max_charge", getIntOption_("max_charge"));
    ff_param.setValue("intensity_threshold", getDoubleOption_("intensity_threshold"));
    iso_ff.setParameters(ff_param);

    FeatureFinder ff;
    ff.setLogType(ProgressLogger::NONE);

    PeakMap exp2 = exp;
    exp2.clear(false);
    for (PeakMap::ConstIterator it = exp.begin(); it != exp.end(); ++it)
    {
      if (it->size() != 0)
      {
        exp2.addSpectrum(*it);
      }
    }

    exp = exp2;
    exp.updateRanges();

    // TODO check MS2 and MS1 counts
    ProgressLogger progresslogger;
    progresslogger.setLogType(log_type_);
    progresslogger.startProgress(0, exp.size(), "Correcting precursor masses");
    for (PeakMap::Iterator it = exp.begin(); it != exp.end(); ++it)
    {
      progresslogger.setProgress(exp.end() - it);
      if (it->getMSLevel() != 2)
      {
        continue;
      }
      // find first MS1 scan of the MS/MS scan
      PeakMap::Iterator ms1_it = it;
      while (ms1_it != exp.begin() && ms1_it->getMSLevel() != 1)
      {
        --ms1_it;
      }
      if (ms1_it == exp.begin() && ms1_it->getMSLevel() != 1)
      {
        writeLog_("Did not find a MS1 scan to the MS/MS scan at RT=" + String(it->getRT()));
        continue;
      }
      if (ms1_it->size() == 0)
      {
        writeDebug_("No peaks in scan at RT=" + String(ms1_it->getRT()) + String(", skipping"), 1);
        continue;
      }

      PeakMap::Iterator ms2_it = ms1_it;
      ++ms2_it;

      while (ms2_it != exp.end() && ms2_it->getMSLevel() == 2)
      {
        // first: error checks
        if (ms2_it->getPrecursors().empty())
        {
          writeDebug_("Warning: found no precursors of spectrum RT=" + String(ms2_it->getRT()) + ", skipping it.", 1);
          ++ms2_it;
          continue;
        }
        else if (ms2_it->getPrecursors().size() > 1)
        {
          writeLog_("Warning: found more than one precursor of spectrum RT=" + String(ms2_it->getRT()) + ", using first one.");
        }

        Precursor prec = *ms2_it->getPrecursors().begin();
        double prec_pos = prec.getMZ();

        PeakMap new_exp;
        // now excise small region from the MS1 spec for the feature finder (isotope pattern must be covered...)
        PeakSpectrum zoom_spec;
        for (PeakSpectrum::ConstIterator pit = ms1_it->begin(); pit != ms1_it->end(); ++pit)
        {
          if (pit->getMZ() > prec_pos - 3 && pit->getMZ() < prec_pos + 3)
          {
            zoom_spec.push_back(*pit);
          }
        }
        new_exp.addSpectrum(zoom_spec);
        new_exp.updateRanges();
        FeatureMap features, seeds;
        ff.run("isotope_wavelet", new_exp, features, ff_param, seeds);
        if (features.empty())
        {
          writeDebug_("No features found for scan RT=" + String(ms1_it->getRT()), 1);
          ++ms2_it;
          continue;
        }

        double max_int(numeric_limits<double>::min());
        double min_dist(numeric_limits<double>::max());
        Size max_int_feat_idx(0);

        for (Size i = 0; i != features.size(); ++i)
        {
          if (fabs(features[i].getMZ() - prec_pos) < precursor_mass_tolerance &&
              features[i].getIntensity() > max_int)
          {
            max_int_feat_idx = i;
            max_int = features[i].getIntensity();
            min_dist = fabs(features[i].getMZ() - prec_pos);
          }
        }


        writeDebug_(" max_int=" + String(max_int) + " mz=" + String(features[max_int_feat_idx].getMZ()) + " charge=" + String(features[max_int_feat_idx].getCharge()), 5);
        if (min_dist < precursor_mass_tolerance)
        {
          prec.setMZ(features[max_int_feat_idx].getMZ());
          prec.setCharge(features[max_int_feat_idx].getCharge());
          vector<Precursor> precs;
          precs.push_back(prec);
          ms2_it->setPrecursors(precs);
          writeDebug_("Correcting precursor mass of spectrum RT=" + String(ms2_it->getRT()) + " from " + String(prec_pos) + " to " + String(prec.getMZ()) + " (z=" + String(prec.getCharge()) + ")", 1);
        }

        ++ms2_it;
      }
      it = --ms2_it;
    }
    progresslogger.endProgress();

    // writing output
    fh.storeExperiment(out, exp, log_type_);

    return EXECUTION_OK;
  }
예제 #2
0
  ExitCodes main_(int, const char **) override
  {

    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    String in = getStringOption_("in");
    String out = getStringOption_("out");

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------

    PeakMap exp;
    MzMLFile f;
    f.load(in, exp);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    //determine maximum peak
    exp.updateRanges();
    double max = exp.getMaxInt() / 100.0;

    for (PeakMap::Iterator it = exp.begin(); it != exp.end(); ++it)
    {
      if (it->getMSLevel() < 2)
      {
        for (PeakMap::SpectrumType::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
        {
          it2->setIntensity(it2->getIntensity() / max);
        }
      }
    }


    /// @todo add chromatogram support for normalization, e.g. for MRM stuff (Andreas)
    /*
      vector<MSChromatogram > chroms = exp.getChromatograms();
      double sum(0);
for (vector<MSChromatogram >::iterator it = chroms.begin(); it != chroms.end(); ++it)
{
  for (MSChromatogram::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
  {
              sum += it2->getIntensity();
          }
      }

      for (vector<MSChromatogram >::iterator it = chroms.begin(); it != chroms.end(); ++it)
      {
          for (MSChromatogram::Iterator it2 = it->begin(); it2 != it->end(); ++it2)
          {
              it2->setIntensity(it2->getIntensity() / sum * 1000000.0);
          }
      }

      exp.setChromatograms(chroms);
    */

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    //annotate output with data processing info
    addDataProcessing_(exp, getProcessingInfo_(DataProcessing::NORMALIZATION));

    f.store(out, exp);

    return EXECUTION_OK;
  }