MRMFeatureAccessOpenMS.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_MRMFEATUREACCESSOPENMS_H
#define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_MRMFEATUREACCESSOPENMS_H

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ITransition.h>

#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h>

#include <boost/shared_ptr.hpp>

// These classes are minimal implementations of the interfaces defined in ITransition:
//  - IFeature
//  - IMRMFeature
//  - ITransitionGroup
//  - ISignalToNoise

namespace OpenMS
{
  class OPENMS_DLLAPI FeatureOpenMS :
    public OpenSwath::IFeature
  {
public:

    explicit FeatureOpenMS(Feature& feature);

    ~FeatureOpenMS();

    void getRT(std::vector<double>& rt);

    void getIntensity(std::vector<double>& intens);

    float getIntensity();

    double getRT();

private:
    Feature* feature_;
  };

  class OPENMS_DLLAPI MRMFeatureOpenMS :
    public OpenSwath::IMRMFeature
  {
public:

    explicit MRMFeatureOpenMS(MRMFeature& mrmfeature);

    ~MRMFeatureOpenMS();

    boost::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID);

    float getIntensity();

    double getRT();

private:
    const MRMFeature& mrmfeature_;
    std::map<std::string, boost::shared_ptr<FeatureOpenMS> > features_;
  };

  template <typename SpectrumT, typename TransitionT>
  class OPENMS_DLLAPI TransitionGroupOpenMS :
    public OpenSwath::ITransitionGroup
  {
public:

    TransitionGroupOpenMS(MRMTransitionGroup<SpectrumT, TransitionT>& trgroup) :
      trgroup_(trgroup)
    {
    }

    ~TransitionGroupOpenMS()
    {
    }

    std::size_t size()
    {
      return trgroup_.size();
    }

    std::vector<std::string> getNativeIDs()
    {
      std::vector<std::string> result;
      for (std::size_t i = 0; i < this->size(); i++)
      {
        result.push_back(trgroup_.getChromatograms()[i].getNativeID());
      }
      return result;
    }

    void getLibraryIntensities(std::vector<double>& intensities)
    {
      trgroup_.getLibraryIntensity(intensities);
    }

private:
    const MRMTransitionGroup<SpectrumT, TransitionT>& trgroup_;
  };

  template <typename PeakT>
  class OPENMS_DLLAPI SignalToNoiseOpenMS :
    public OpenSwath::ISignalToNoise
  {
public:

    SignalToNoiseOpenMS(OpenMS::MSSpectrum<PeakT>& chromat,
                        double sn_win_len_, unsigned int sn_bin_count_) :
      chromatogram_(chromat), sn_()
    {
      OpenMS::Param snt_parameters = sn_.getParameters();
      snt_parameters.setValue("win_len", sn_win_len_);
      snt_parameters.setValue("bin_count", sn_bin_count_);
      sn_.setParameters(snt_parameters);
      sn_.init(chromatogram_);
    }

    double getValueAtRT(double RT)
    {
      typename OpenMS::MSSpectrum<PeakT>::const_iterator it = chromatogram_.MZBegin(RT);
      return sn_.getSignalToNoise(*it);
    }

private:
    const OpenMS::MSSpectrum<PeakT>& chromatogram_;
    OpenMS::SignalToNoiseEstimatorMedian<OpenMS::MSSpectrum<PeakT> > sn_;
  };

}

#endif