PeptideAndProteinQuant.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>

namespace OpenMS
{
  class OPENMS_DLLAPI PeptideAndProteinQuant :
    public DefaultParamHandler
  {
public:

    typedef std::map<UInt64, double> SampleAbundances;

    struct PeptideData
    {
      std::map<Int, std::map<Int, SampleAbundances>> abundances;

      SampleAbundances total_abundances;

      std::set<String> accessions;

      Size id_count;

      PeptideData() :
        id_count(0) {}
    };

    typedef std::map<AASequence, PeptideData> PeptideQuant;

    struct ProteinData
    {
      std::map<String, SampleAbundances> abundances;

      SampleAbundances total_abundances;

      Size id_count;

      ProteinData() :
        id_count(0) {}
    };

    typedef std::map<String, ProteinData> ProteinQuant;

    struct Statistics
    {
      Size n_samples;

      Size n_fractions;

      Size n_ms_files;

      Size quant_proteins, too_few_peptides;

      Size quant_peptides, total_peptides;

      Size quant_features, total_features, blank_features, ambig_features;

      Statistics() :
        n_samples(0), quant_proteins(0), too_few_peptides(0),
        quant_peptides(0), total_peptides(0), quant_features(0),
        total_features(0), blank_features(0), ambig_features(0) {}
    };

    PeptideAndProteinQuant();

    ~PeptideAndProteinQuant() override {}

    void readQuantData(FeatureMap& features, const ExperimentalDesign& ed);

    void readQuantData(ConsensusMap& consensus, const ExperimentalDesign& ed);

    void readQuantData(std::vector<ProteinIdentification>& proteins,
                       std::vector<PeptideIdentification>& peptides,
                       const ExperimentalDesign& ed);

    void quantifyPeptides(const std::vector<PeptideIdentification>& peptides =
                          std::vector<PeptideIdentification>());


    void quantifyProteins(const ProteinIdentification& proteins = 
                          ProteinIdentification());

    const Statistics& getStatistics();

    const PeptideQuant& getPeptideResults();

    const ProteinQuant& getProteinResults();

    static void annotateQuantificationsToProteins(
      const ProteinQuant& protein_quants, 
      ProteinIdentification& proteins,
      const UInt n_samples);

private:

    Statistics stats_;

    PeptideQuant pep_quant_;

    ProteinQuant prot_quant_;


    PeptideHit getAnnotation_(std::vector<PeptideIdentification>& peptides);

    void quantifyFeature_(const FeatureHandle& feature, 
      size_t fraction, 
      size_t sample, 
      const PeptideHit& hit);

    /*
     *   @brief Determine fraction and charge state of a peptide with the highest
     *   number of abundances.
     *   @return true if at least one abundance was found, false otherwise
     */ 
    bool getBest_(
      const std::map<Int, std::map<Int, SampleAbundances>> & peptide_abundances, 
      std::pair<size_t, size_t> & best)
    {
      size_t best_n_quant(0);
      double best_abundance(0);
      best = std::make_pair(0,0);

      for (auto & fa : peptide_abundances)  // for all fractions 
      {
        for (auto & ca : fa.second) // for all charge states
        {
          const Int & fraction = fa.first;
          const Int & charge = ca.first;

          double current_abundance(0);
          for (auto & sa : ca.second) // loop over abundances
          {
            const double & sample_abundance = sa.second;
            current_abundance += sample_abundance;
          }

          if (current_abundance <= 0) { continue; }

          const size_t current_n_quant = ca.second.size();
          if (current_n_quant > best_n_quant)
          {           
            best_abundance = current_abundance;
            best_n_quant = current_n_quant;
            best = std::make_pair(fraction, charge);
          }
          else if (current_n_quant == best_n_quant 
            && current_abundance > best_abundance)  // resolve tie by abundance
          {
            best_abundance = current_abundance;
            best = std::make_pair(fraction, charge);
          }
        }
      }
      if (best_abundance <= 0) { return false; } // only identified, not quantified
      return true;
    }

    template <typename T>
    void orderBest_(const std::map<T, SampleAbundances> & abundances,
                    std::vector<T>& result)
    {
      typedef std::pair<Size, double> PairType;
      std::multimap<PairType, T, std::greater<PairType> > order;
      for (typename std::map<T, SampleAbundances>::const_iterator ab_it =
             abundances.begin(); ab_it != abundances.end(); ++ab_it)
      {
        double total = 0.0;
        for (SampleAbundances::const_iterator samp_it = ab_it->second.begin();
             samp_it != ab_it->second.end(); ++samp_it)
        {
          total += samp_it->second;
        }
        if (total <= 0.0) continue;         // not quantified
        PairType key = std::make_pair(ab_it->second.size(), total);
        order.insert(std::make_pair(key, ab_it->first));
      }
      result.clear();
      for (typename std::multimap<PairType, T, std::greater<PairType> >::
           iterator ord_it = order.begin(); ord_it != order.end(); ++ord_it)
      {
        result.push_back(ord_it->second);
      }
    }



    void normalizePeptides_();

    String getAccession_(const std::set<String>& pep_accessions,
                         std::map<String, String>& accession_to_leader);

    void countPeptides_(std::vector<PeptideIdentification>& peptides);

    void updateMembers_() override;

  };   // class

} // namespace