MRMTransitionGroup.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: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

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

namespace OpenMS
{

  template <typename ChromatogramType, typename TransitionType>
  class MRMTransitionGroup
  {

public:


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

    MRMTransitionGroup()
    {
    }

    MRMTransitionGroup(const MRMTransitionGroup & rhs) :
      tr_gr_id_(rhs.tr_gr_id_),
      transitions_(rhs.transitions_),
      chromatograms_(rhs.chromatograms_),
      precursor_chromatograms_(rhs.precursor_chromatograms_),
      mrm_features_(rhs.mrm_features_),
      chromatogram_map_(rhs.chromatogram_map_),
      precursor_chromatogram_map_(rhs.precursor_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_;
        precursor_chromatograms_ = rhs.precursor_chromatograms_;
        mrm_features_ = rhs.mrm_features_;
        transition_map_ = rhs.transition_map_;
        chromatogram_map_ = rhs.chromatogram_map_;
        precursor_chromatogram_map_ = rhs.precursor_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 bool hasTransition(String key) const
    {
      return transition_map_.find(key) != transition_map_.end();
    }

    inline const TransitionType & getTransition(String key)
    {
      OPENMS_PRECONDITION(hasTransition(key), "Cannot retrieve transitions that does not exist")
      OPENMS_PRECONDITION(transitions_.size() > (size_t)transition_map_[key], "Mapping needs to be accurate")
      return transitions_[transition_map_[key]];
    }



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

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

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

      // OPENMS_POSTCONDITION(chromatogramIdsMatch(), "Chromatogam ids do not match")
    }

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

    inline ChromatogramType & getChromatogram(const String& key)
    {
      OPENMS_PRECONDITION(hasChromatogram(key), "Cannot retrieve chromatogram that does not exist")
      OPENMS_PRECONDITION(chromatograms_.size() > (size_t)chromatogram_map_[key], "Mapping needs to be accurate")
      return chromatograms_[chromatogram_map_[key]];
    }

    inline const ChromatogramType & getChromatogram(const String& key) const
    {
      OPENMS_PRECONDITION(hasChromatogram(key), "Cannot retrieve chromatogram that does not exist")
      OPENMS_PRECONDITION(chromatograms_.size() > (size_t)chromatogram_map_.at(key), "Mapping needs to be accurate")
      return chromatograms_[chromatogram_map_.at(key)];
    }



    inline std::vector<ChromatogramType> & getPrecursorChromatograms()
    {
      return precursor_chromatograms_;
    }

    inline const std::vector<ChromatogramType> & getPrecursorChromatograms() const
    {
      return precursor_chromatograms_;
    }

    inline void addPrecursorChromatogram(const ChromatogramType & chromatogram, const String& key)
    {
      precursor_chromatograms_.push_back(chromatogram);
      precursor_chromatogram_map_[key] = boost::numeric_cast<int>(precursor_chromatograms_.size()) - 1;

      // OPENMS_POSTCONDITION(chromatogramIdsMatch(), "Chromatogram ids do not match")
    }

    inline bool hasPrecursorChromatogram(const String& key) const
    {
      return precursor_chromatogram_map_.find(key) != precursor_chromatogram_map_.end();
    }

    inline ChromatogramType & getPrecursorChromatogram(const String& key)
    {
      OPENMS_PRECONDITION(hasPrecursorChromatogram(key), "Cannot retrieve precursor chromatogram that does not exist")
      OPENMS_PRECONDITION(precursor_chromatograms_.size() > (size_t)precursor_chromatogram_map_.at(key), "Mapping needs to be accurate")
      return precursor_chromatograms_[precursor_chromatogram_map_[key]];
    }

    inline const ChromatogramType & getPrecursorChromatogram(const String& key) const
    {
      OPENMS_PRECONDITION(hasPrecursorChromatogram(key), "Cannot retrieve precursor chromatogram that does not exist")
      OPENMS_PRECONDITION(precursor_chromatograms_.size() > (size_t)precursor_chromatogram_map_.at(key), "Mapping needs to be accurate")
      return precursor_chromatograms_[precursor_chromatogram_map_.at(key)];
    }



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

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

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




    inline bool isInternallyConsistent() const
    {
      OPENMS_PRECONDITION(transitions_.size() == chromatograms_.size(), "Same number of transitions as chromatograms are required")
      OPENMS_PRECONDITION(transition_map_.size() == chromatogram_map_.size(), "Same number of transitions as chromatograms mappings are required")
      OPENMS_PRECONDITION(isMappingConsistent_(), "Mapping needs to be consistent")
      return true;
    }

    inline bool chromatogramIdsMatch() const
    {
      for (std::map<String, int>::const_iterator it = chromatogram_map_.begin(); it != chromatogram_map_.end(); it++)
      {
        if (getChromatogram(it->first).getNativeID() != it->first)
        {
          return false;
        }
      }
      for (std::map<String, int>::const_iterator it = precursor_chromatogram_map_.begin(); it != precursor_chromatogram_map_.end(); it++)
      {
        if (getPrecursorChromatogram(it->first).getNativeID() != it->first)
        {
          return false;
        }
      }
      return true;
    }

    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;
        }
      }
    }

    MRMTransitionGroup subset(std::vector<std::string> tr_ids) const
    {
      MRMTransitionGroup transition_group_subset;
      transition_group_subset.setTransitionGroupID(tr_gr_id_);

      for (typename TransitionsType::const_iterator tr_it = transitions_.begin(); tr_it != transitions_.end(); ++tr_it)
      {
        if (std::find(tr_ids.begin(), tr_ids.end(), tr_it->getNativeID()) != tr_ids.end())
        {
          if (this->hasTransition(tr_it->getNativeID()))
          {
            transition_group_subset.addTransition(*tr_it, tr_it->getNativeID());
          }
          if (this->hasChromatogram(tr_it->getNativeID()))
          {
            transition_group_subset.addChromatogram(chromatograms_[chromatogram_map_.at(tr_it->getNativeID())], tr_it->getNativeID());
          }
        }
      }

      for (typename std::vector<ChromatogramType>::const_iterator pr_it = precursor_chromatograms_.begin(); pr_it != precursor_chromatograms_.end(); ++pr_it)
      {
        // add precursor chromatograms if present
        transition_group_subset.addPrecursorChromatogram(*pr_it,pr_it->getNativeID());
      }

      for (std::vector< MRMFeature >::const_iterator tgf_it = mrm_features_.begin(); tgf_it != mrm_features_.end(); ++tgf_it)
      {
        MRMFeature mf;
        mf.setIntensity(tgf_it->getIntensity());
        mf.setRT(tgf_it->getRT());
        std::vector<String> metavalues;
        tgf_it->getKeys(metavalues);
        for (std::vector<String>::iterator key_it = metavalues.begin(); key_it != metavalues.end(); ++key_it)
        {
          mf.setMetaValue(*key_it,tgf_it->getMetaValue(*key_it));
        }
        for (typename TransitionsType::const_iterator tr_it = transitions_.begin(); tr_it != transitions_.end(); ++tr_it)
        {
          if (std::find(tr_ids.begin(), tr_ids.end(), tr_it->getNativeID()) != tr_ids.end())
          {
            mf.addFeature(tgf_it->getFeature(tr_it->getNativeID()),tr_it->getNativeID());
          }
        }
        std::vector<String> pf_ids;
        tgf_it->getPrecursorFeatureIDs(pf_ids);
        for (std::vector<String>::iterator pf_ids_it = pf_ids.begin(); pf_ids_it != pf_ids.end(); ++pf_ids_it)
        {
          mf.addPrecursorFeature(tgf_it->getPrecursorFeature(*pf_ids_it), *pf_ids_it);
        }
        transition_group_subset.addFeature(mf);
      }

      return transition_group_subset;
    }

    MRMTransitionGroup subsetDependent(std::vector<std::string> tr_ids) const
    {
      MRMTransitionGroup transition_group_subset;
      transition_group_subset.setTransitionGroupID(tr_gr_id_);

      for (typename TransitionsType::const_iterator tr_it = transitions_.begin(); tr_it != transitions_.end(); ++tr_it)
      {
        if (std::find(tr_ids.begin(), tr_ids.end(), tr_it->getNativeID()) != tr_ids.end())
        {
          transition_group_subset.addTransition(*tr_it, tr_it->getNativeID());
          transition_group_subset.addChromatogram(chromatograms_[chromatogram_map_.at(tr_it->getNativeID())], tr_it->getNativeID());
        }
      }

      for (std::vector< MRMFeature >::const_iterator tgf_it = mrm_features_.begin(); tgf_it != mrm_features_.end(); ++tgf_it)
      {
        transition_group_subset.addFeature(*tgf_it);
      }

      return transition_group_subset;
    }

    const MRMFeature& getBestFeature() const
    {
      OPENMS_PRECONDITION(!getFeatures().empty(), "Cannot get best feature for empty transition group")

      // Find the feature with the highest score
      Size bestf = 0;
      double highest_score = getFeatures()[0].getOverallQuality();
      for (Size it = 0; it < getFeatures().size(); it++)
      {
        if (getFeatures()[it].getOverallQuality() > highest_score)
        {
          bestf = it;
          highest_score = getFeatures()[it].getOverallQuality();
        }
      }
      return getFeatures()[bestf];
    }

protected:

    bool isMappingConsistent_() const
    {
      if (transition_map_.size() != chromatogram_map_.size()) 
      {
        return false;
      }
      for (std::map<String, int>::const_iterator it = chromatogram_map_.begin(); it != chromatogram_map_.end(); it++)
      {
        if (!hasTransition(it->first)) 
        {
          return false;
        }
      }
      return true;
    }

    String tr_gr_id_;

    TransitionsType transitions_;

    std::vector<ChromatogramType> chromatograms_;

    std::vector<ChromatogramType> precursor_chromatograms_;

    MRMFeatureListType mrm_features_;

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

  };
}