ChromatogramTools.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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#pragma once

#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/RangeUtils.h>
#include <OpenMS/CONCEPT/LogStream.h>

namespace OpenMS
{
  class ChromatogramTools
  {
public:

    ChromatogramTools()
    {}

    ChromatogramTools(const ChromatogramTools & /*rhs*/)
    {}

    virtual ~ChromatogramTools()
    {}




    template <typename ExperimentType>
    void convertChromatogramsToSpectra(ExperimentType & exp)
    {
      for (std::vector<MSChromatogram >::const_iterator it = exp.getChromatograms().begin(); it != exp.getChromatograms().end(); ++it)
      {
        // for each peak add a new spectrum
        for (typename ExperimentType::ChromatogramType::const_iterator pit = it->begin(); pit != it->end(); ++pit)
        {
          typename ExperimentType::SpectrumType spec;

          // add precursor and product peaks to spectrum settings
          spec.getPrecursors().push_back(it->getPrecursor());
          spec.getProducts().push_back(it->getProduct());
          spec.setRT(pit->getRT());
          spec.setMSLevel(2);
          spec.setInstrumentSettings(it->getInstrumentSettings());
          spec.setAcquisitionInfo(it->getAcquisitionInfo());
          spec.setSourceFile(it->getSourceFile());

          // TODO implement others
          if (it->getChromatogramType() == ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM)
          {
            spec.getInstrumentSettings().setScanMode(InstrumentSettings::SRM);
          }
          if (it->getChromatogramType() == ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM)
          {
            spec.getInstrumentSettings().setScanMode(InstrumentSettings::SIM);
          }

          // new spec contains one peak, with product m/z and intensity
          typename ExperimentType::PeakType peak;
          peak.setMZ(it->getMZ());
          peak.setIntensity(pit->getIntensity());
          spec.push_back(peak);
          exp.addSpectrum(spec);
        }
      }

      exp.setChromatograms(std::vector<MSChromatogram >());
    }

    template <typename ExperimentType>
    void convertSpectraToChromatograms(ExperimentType & exp, bool remove_spectra = false, bool force_conversion = false)
    {
      typedef typename ExperimentType::SpectrumType SpectrumType;
      Map<double, Map<double, std::vector<SpectrumType> > > chroms;
      Map<double, MSChromatogram > chroms_xic;
      for (typename ExperimentType::ConstIterator it = exp.begin(); it != exp.end(); ++it)
      {
        // TODO other types
        if (it->getInstrumentSettings().getScanMode() == InstrumentSettings::SRM || force_conversion)
        {
          // exactly one precursor and one product ion
          if (it->getPrecursors().size() == 1 && it->size() == 1)
          {
            chroms[it->getPrecursors().begin()->getMZ()][it->begin()->getMZ()].push_back(*it);
          }
          // Exactly one precursor and more than one product ion.
          // This is how some converters (e.g. ReAdW 4.0.2) store SRM data,
          // collecting all information from one precursor in a single
          // pseudo-spectrum
          else if (it->getPrecursors().size() == 1 && it->size() > 0)
          {
            for (Size peak_idx = 0; peak_idx < it->size(); peak_idx++)
            {
              // copy spectrum and delete all data, but keep metadata, then add single peak
              SpectrumType dummy = *it;
              dummy.clear(false);
              dummy.push_back((*it)[peak_idx]);
              chroms[it->getPrecursors().begin()->getMZ()][(*it)[peak_idx].getMZ()].push_back(dummy);
            }
          }
          // We have no precursor, so this may be a MS1 chromatogram scan (as encountered in GC-MS)
          else if (force_conversion)
          {
            for (auto& p : *it)
            {
              double mz = p.getMZ();
              ChromatogramPeak chr_p;
              chr_p.setRT(it->getRT());
              chr_p.setIntensity(p.getIntensity());
              if (chroms_xic.find(mz) == chroms_xic.end())
              {
                // new chromatogram
                chroms_xic[mz].getPrecursor().setMZ(mz);
                // chroms_xic[mz].setProduct(prod); // probably no product
                chroms_xic[mz].setInstrumentSettings(it->getInstrumentSettings());
                chroms_xic[mz].getPrecursor().setMetaValue("description", String("XIC @ " + String(mz)));
                chroms_xic[mz].setAcquisitionInfo(it->getAcquisitionInfo());
                chroms_xic[mz].setSourceFile(it->getSourceFile());
              }
              chroms_xic[mz].push_back(chr_p);
            }
          }
          else
          {
            LOG_WARN << "ChromatogramTools: need exactly one precursor (given " << it->getPrecursors().size() <<
            ") and one or more product ions (" << it->size() << "), skipping conversion of this spectrum to chromatogram. If this is a MS1 chromatogram, please force conversion (e.g. with -convert_to_chromatograms)." << std::endl;
          }
        }
        else
        {
          // This does not makes sense to warn here, because it would also warn on simple mass spectra...
          // TODO think what to to here
          //LOG_WARN << "ChromatogramTools: cannot convert other chromatogram spectra types than 'Selected Reaction Monitoring', skipping conversion." << std::endl;
          //
        }
      }

      // Add the XIC chromatograms
      for (auto & chrom: chroms_xic) exp.addChromatogram(chrom.second);

      // Add the SRM chromatograms
      typename Map<double, Map<double, std::vector<SpectrumType> > >::const_iterator it1 = chroms.begin();
      for (; it1 != chroms.end(); ++it1)
      {
        typename Map<double, std::vector<SpectrumType> >::const_iterator it2 = it1->second.begin();
        for (; it2 != it1->second.end(); ++it2)
        {
          typename ExperimentType::ChromatogramType chrom;
          chrom.setPrecursor(*it2->second.begin()->getPrecursors().begin());
          Product prod;
          prod.setMZ(it2->first);
          chrom.setProduct(prod);
          chrom.setInstrumentSettings(it2->second.begin()->getInstrumentSettings());
          chrom.setAcquisitionInfo(it2->second.begin()->getAcquisitionInfo());
          chrom.setSourceFile(it2->second.begin()->getSourceFile());

          typename std::vector<SpectrumType>::const_iterator it3 = it2->second.begin();
          for (; it3 != it2->second.end(); ++it3)
          {
            typename ExperimentType::ChromatogramType::PeakType p;
            p.setRT(it3->getRT());
            p.setIntensity(it3->begin()->getIntensity());
            chrom.push_back(p);
          }

          chrom.setNativeID("chromatogram=" + it2->second.begin()->getNativeID());               // TODO native id?
          chrom.setChromatogramType(ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM);
          exp.addChromatogram(chrom);
        }
      }

      if (remove_spectra)
      {
        exp.getSpectra().erase(remove_if(exp.begin(), exp.end(), HasScanMode<SpectrumType>(InstrumentSettings::SRM)), exp.end());
      }
    }

  };
} // namespace OpenMS