MRMDecoy.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.
//
// 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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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/assign.hpp>
#include <boost/random/mersenne_twister.hpp>
#include <boost/random/uniform_int.hpp>
#include <boost/random/variate_generator.hpp>
#include <boost/unordered_map.hpp>

#include <string>
#include <vector>
#include <map>
#include <utility> // for pair

// #define DEBUG_MRMDECOY

namespace OpenMS
{
  class OPENMS_DLLAPI MRMDecoy :
    public DefaultParamHandler,
    public ProgressLogger
  {

public:

    typedef std::vector<size_t> IndexType;

    MRMDecoy();

    void generateDecoys(const OpenMS::TargetedExperiment& exp,
                        OpenMS::TargetedExperiment& dec,
                        const String& method,
                        const double aim_decoy_fraction,
                        const bool switchKR,
                        const String& decoy_tag,
                        const int max_attempts,
                        const double identity_threshold,
                        const double precursor_mz_shift,
                        const double product_mz_shift,
                        const double product_mz_threshold,
                        const std::vector<String>& fragment_types,
                        const std::vector<size_t>& fragment_charges,
                        const bool enable_specific_losses,
                        const bool enable_unspecific_losses,
                        const int round_decPow = -4) const;

    typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
    typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
    typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;

    typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType;

    float AASequenceIdentity(const String& sequence, const String& decoy) const;

    OpenMS::TargetedExperiment::Peptide shufflePeptide(
                OpenMS::TargetedExperiment::Peptide peptide,
                const double identity_threshold,
                int seed = -1,
                const int max_attempts = 100) const;

    static OpenMS::TargetedExperiment::Peptide reversePeptide(
                const OpenMS::TargetedExperiment::Peptide& peptide,
                const bool keepN,
                const bool keepC, 
                const String& const_pattern = String());

    static IndexType findFixedResidues(const std::string& sequence,
        bool keepN, bool keepC, const OpenMS::String& keep_const_pattern);

protected:

    bool hasCNterminalMods_(const OpenMS::TargetedExperiment::Peptide& peptide, bool checkCterminalAA) const;

    IndexType findFixedResidues_(const std::string& sequence) const;

    IndexType findFixedAndTermResidues_(const std::string& sequence) const;

    OpenMS::TargetedExperiment::Peptide pseudoreversePeptide_(
      const OpenMS::TargetedExperiment::Peptide& peptide) const;

    OpenMS::TargetedExperiment::Peptide reversePeptide_(
      const OpenMS::TargetedExperiment::Peptide& peptide) const;

    void updateMembers_() override;

    String keep_const_pattern_;
    bool keepN_;
    bool keepC_;
  };
}