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 2002-2020.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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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);
 
    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 = std::accumulate(
              std::begin(ca.second),
              std::end(ca.second),
              0.0,
              [] (int value, const SampleAbundances::value_type& p)
              { return value + p.second; }
          ); // loop over abundances
 
          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);
          }
        }
      }
      return best_abundance > 0.;
    }
 
    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