ChromatogramTools.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#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>
 
#include <map>
 
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::ChromatogramType::SELECTED_REACTION_MONITORING_CHROMATOGRAM)
          {
            spec.getInstrumentSettings().setScanMode(InstrumentSettings::ScanMode::SRM);
          }
          if (it->getChromatogramType() == ChromatogramSettings::ChromatogramType::SELECTED_ION_MONITORING_CHROMATOGRAM)
          {
            spec.getInstrumentSettings().setScanMode(InstrumentSettings::ScanMode::SIM);
          }
 
          // new spec contains one peak, with product m/z and intensity
          spec.emplace_back(it->getMZ(), pit->getIntensity());
          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;
      std::map<double, std::map<double, std::vector<SpectrumType> > > chroms;
      std::map<double, MSChromatogram > chroms_xic;
      for (typename ExperimentType::ConstIterator it = exp.begin(); it != exp.end(); ++it)
      {
        // TODO other types
        if (it->getInstrumentSettings().getScanMode() == InstrumentSettings::ScanMode::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]);
              // the chromatograms of one spectrum would share its native ID otherwise (mzML requires unique ids)
              dummy.setNativeID(it->getNativeID() + " product=" + StringUtils::toStr((*it)[peak_idx].getMZ()));
              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.contains(mz))
              {
                // new chromatogram; the native ID must be unique (mzML requires it) and the m/z is the key here
                chroms_xic[mz].setNativeID("XIC mz=" + StringUtils::toStr(mz));
                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",std::string("XIC @ " + StringUtils::toStr(mz)));
                chroms_xic[mz].setAcquisitionInfo(it->getAcquisitionInfo());
                chroms_xic[mz].setSourceFile(it->getSourceFile());
              }
              chroms_xic[mz].push_back(chr_p);
            }
          }
          else
          {
            OPENMS_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
          //OPENMS_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 std::map<double, std::map<double, std::vector<SpectrumType> > >::const_iterator it1 = chroms.begin();
      for (; it1 != chroms.end(); ++it1)
      {
        typename std::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::ChromatogramType::SELECTED_REACTION_MONITORING_CHROMATOGRAM);
          exp.addChromatogram(chrom);
        }
      }
 
      if (remove_spectra)
      {
        exp.getSpectra().erase(remove_if(exp.begin(), exp.end(), HasScanMode<SpectrumType>(static_cast<Int>(InstrumentSettings::ScanMode::SRM))), exp.end());
      }
    }
 
  };
} // namespace OpenMS