MRMDecoy.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_MRMDECOY_H
#define OPENMS_ANALYSIS_OPENSWATH_MRMDECOY_H

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.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 <map>
#include <string>
#include <vector>
#include <utility> // for pair

// #define DEBUG_MRMDECOY

namespace OpenMS
{
  class OPENMS_DLLAPI MRMDecoy :
    public ProgressLogger
  {
public:
    MRMDecoy() {} // empty, no members

    void generateDecoys(OpenMS::TargetedExperiment& exp,
                        OpenMS::TargetedExperiment& dec, String method, String decoy_tag,
                        double identity_threshold, int max_attempts, double mz_threshold, 
                        bool theoretical, double mz_shift, bool exclude_similar, 
                        double similarity_threshold, bool remove_CNterm_mods);

    void restrictTransitions(OpenMS::TargetedExperiment& exp, int min_transitions,
                             int max_transitions);

    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::map<String, double> > IonSeries;
    typedef std::map<String, IonSeries> IonSeriesMapType;

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

    std::pair<String, DoubleReal> getDecoyIon(String ionid,
                                              std::map<String, std::map<String, DoubleReal> >& decoy_ionseries);

    std::pair<String, double> getTargetIon(double ProductMZ, double mz_threshold,
                                           std::map<String, std::map<String, double> > target_ionseries);

    std::map<String, std::map<String, double> > getIonSeries(
      AASequence sequence, int precursor_charge, int max_isotopes = 2);

    std::vector<std::pair<std::string::size_type, std::string> > find_all_tryptic(
      std::string sequence);

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

    bool has_CNterminal_mods(const OpenMS::TargetedExperiment::Peptide & peptide);

    void correctMasses(OpenMS::TargetedExperiment& exp, double mz_threshold);

    OpenMS::TargetedExperiment::Peptide shufflePeptide(
      OpenMS::TargetedExperiment::Peptide peptide, double identity_threshold, int seed = -1,
      int max_attempts = 10);

    OpenMS::TargetedExperiment::Peptide pseudoreversePeptide(
      OpenMS::TargetedExperiment::Peptide peptide);

    OpenMS::TargetedExperiment::Peptide reversePeptide(
      OpenMS::TargetedExperiment::Peptide peptide);
  };
}

#endif