PeptideAndProteinQuant.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H
#define OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H

#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>

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

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

    struct PeptideData
    {
      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 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() {}

    void quantifyPeptides(FeatureMap<> & features);

    void quantifyPeptides(ConsensusMap & consensus);

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

    const Statistics & getStatistics();

    const PeptideQuant & getPeptideResults();

    const ProteinQuant & getProteinResults();

private:

    Statistics stats_;

    PeptideQuant pep_quant_;

    ProteinQuant prot_quant_;


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

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

    template <typename T>
    void orderBest_(const std::map<T, SampleAbundances> abundances,
                    std::vector<T> & result)
    {
      typedef std::pair<Size, DoubleReal> 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)
      {
        DoubleReal 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 quantifyPeptides_();

    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_();

  };   // class

} // namespace

#endif // OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H