MRMTransitionGroup.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#ifndef OPENMS_KERNEL_MRMTRANSITIONGROUP_H
#define OPENMS_KERNEL_MRMTRANSITIONGROUP_H

#include <OpenMS/KERNEL/MRMFeature.h>
#include <boost/numeric/conversion/cast.hpp>

namespace OpenMS
{
  template <typename SpectrumType, typename TransitionType>
  class MRMTransitionGroup
  {

public:



    typedef std::vector<MRMFeature> MRMFeatureListType;
    typedef std::vector<TransitionType> TransitionsType;
    typedef typename SpectrumType::PeakType PeakType;

    MRMTransitionGroup()
    {
    }

    MRMTransitionGroup(const MRMTransitionGroup & rhs) :
      tr_gr_id_(rhs.tr_gr_id_),
      transitions_(rhs.transitions_),
      chromatograms_(rhs.chromatograms_),
      cons_features_(rhs.cons_features_),
      chromatogram_map_(rhs.chromatogram_map_),
      transition_map_(rhs.transition_map_)
    {
    }

    virtual ~MRMTransitionGroup()
    {
    }

    MRMTransitionGroup & operator=(const MRMTransitionGroup & rhs)
    {
      if (&rhs != this)
      {
        tr_gr_id_ = rhs.tr_gr_id_;
        transitions_ = rhs.transitions_;
        chromatograms_ = rhs.chromatograms_;
        cons_features_ = rhs.cons_features_;

        transition_map_ = rhs.transition_map_;
        chromatogram_map_ = rhs.chromatogram_map_;
      }
      return *this;
    }

    inline Size size() const
    {
      return chromatograms_.size();
    }

    inline const String & getTransitionGroupID() const
    {
      return tr_gr_id_;
    }

    inline void setTransitionGroupID(const String & tr_gr_id)
    {
      tr_gr_id_ = tr_gr_id;
    }

    inline const std::vector<TransitionType> & getTransitions() const
    {
      return transitions_;
    }

    inline std::vector<TransitionType> & getTransitionsMuteable()
    {
      return transitions_;
    }

    inline void addTransition(const TransitionType & transition, String key)
    {
      transitions_.push_back(transition);
      transition_map_[key] = boost::numeric_cast<int>(transitions_.size()) - 1;
    }

    inline const TransitionType & getTransition(String key) 
    {
      return transitions_[transition_map_[key]];
    }

    inline bool hasTransition(String key)
    {
      return transition_map_.find(key) != transition_map_.end();
    }

    inline const std::vector<SpectrumType> & getChromatograms() const
    {
      return chromatograms_;
    }

    inline std::vector<SpectrumType> & getChromatograms()
    {
      return chromatograms_;
    }

    inline void addChromatogram(SpectrumType & chromatogram, String key)
    {
      chromatograms_.push_back(chromatogram);
      chromatogram_map_[key] = boost::numeric_cast<int>(chromatograms_.size()) - 1;
    }

    inline SpectrumType & getChromatogram(String key)
    {
      return chromatograms_[chromatogram_map_[key]];
    }

    inline bool hasChromatogram(String key)
    {
      return chromatogram_map_.find(key) != chromatogram_map_.end();
    }

    inline const std::vector<MRMFeature> & getFeatures() const
    {
      return cons_features_;
    }

    inline std::vector<MRMFeature> & getFeaturesMuteable()
    {
      return cons_features_;
    }

    inline void addFeature(MRMFeature & feature)
    {
      cons_features_.push_back(feature);
    }

    void getLibraryIntensity(std::vector<double> & result) const
    {
      for (typename TransitionsType::const_iterator it = transitions_.begin(); it != transitions_.end(); ++it)
      {
        result.push_back(it->getLibraryIntensity());
      }
      for (Size i = 0; i < result.size(); i++)
      {
        // the library intensity should never be below zero
        if (result[i] < 0.0) 
        {
          result[i] = 0.0;
        }
      }
    }

protected:

    String tr_gr_id_;

    TransitionsType transitions_;

    std::vector<SpectrumType> chromatograms_;

    MRMFeatureListType cons_features_;

    std::map<String, int> chromatogram_map_;
    std::map<String, int> transition_map_;

  };
}
#endif