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 2002-2022.
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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;

      std::map<Int, std::map<Int, SampleAbundances>> psm_counts;

      SampleAbundances total_abundances;

      SampleAbundances total_psm_counts;

      std::set<String> accessions;

      Size psm_count = 0;

      PeptideData() = default;
    };

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

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

      std::map<String, SampleAbundances> psm_counts;

      SampleAbundances total_abundances;

      SampleAbundances total_psm_counts;

      SampleAbundances total_distinct_peptides;

      Size psm_count = 0;

      ProteinData() = default;
    };

    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();

    void annotateQuantificationsToProteins(
      const ProteinQuant& protein_quants, 
      ProteinIdentification& proteins,
      bool remove_unquantified = true);

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);

    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