MRMTransitionGroup.h

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// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#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, const String& key)
    {
      // store the index where to find the transition, using the key for lookup
      auto result = transition_map_.emplace(key, int(transitions_.size()));
      if (!result.second) // ouch: key was already used
      {
        throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Internal error: Transition with nativeID was already present!", key);
      }
      transitions_.push_back(transition);
    }
 
    inline bool hasTransition(const String& key) const
    {
      return transition_map_.find(key) != transition_map_.end();
    }
 
    inline const TransitionType& getTransition(const 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)
    {
      // store the index where to find the chromatogram, using the key for lookup
      auto result = chromatogram_map_.emplace(key, int(chromatograms_.size()));
      if (!result.second) // ouch: key was already used
      {
        throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Internal error: Chromatogram with nativeID was already present!", key);
      }
      chromatograms_.push_back(chromatogram);
    }
 
    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_.at(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)
    {
      // store the index where to find the chromatogram, using the key for lookup
      auto result = precursor_chromatogram_map_.emplace(key, int(precursor_chromatograms_.size()));
      if (!result.second) // ouch: key was already used
      {
        throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Internal error: Chromatogram with nativeID was already present!", key);
      }
      precursor_chromatograms_.push_back(chromatogram);
    }
 
    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_.at(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 void addFeature(MRMFeature && feature)
    {
      mrm_features_.push_back(std::move(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 (const auto& tr : transitions_)
      {
        if (std::find(tr_ids.begin(), tr_ids.end(), tr.getNativeID()) != tr_ids.end())
        {
          if (this->hasTransition(tr.getNativeID()))
          {
            transition_group_subset.addTransition(tr, tr.getNativeID());
          }
          if (this->hasChromatogram(tr.getNativeID()))
          {
            transition_group_subset.addChromatogram(chromatograms_[chromatogram_map_.at(tr.getNativeID())], tr.getNativeID());
          }
        }
      }
 
      for (const auto& pc : precursor_chromatograms_)
      {
        // add precursor chromatograms if present
        transition_group_subset.addPrecursorChromatogram(pc, pc.getNativeID());
      }
 
      for (const auto& tgf : mrm_features_)
      {
        MRMFeature mf;
        mf.setIntensity(tgf.getIntensity());
        mf.setRT(tgf.getRT());
        mf.MetaInfoInterface::operator=(tgf);
 
        for (const auto& tr : transitions_)
        {
          if (std::find(tr_ids.begin(), tr_ids.end(), tr.getNativeID()) != tr_ids.end())
          {
            mf.addFeature(tgf.getFeature(tr.getNativeID()),tr.getNativeID());
          }
        }
        std::vector<String> pf_ids;
        tgf.getPrecursorFeatureIDs(pf_ids);
        for (const auto& pf_id : pf_ids)
        {
          mf.addPrecursorFeature(tgf.getPrecursorFeature(pf_id), pf_id);
        }
        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_;
 
  };
}