MRMDecoy.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_MRMDECOY_H
#define OPENMS_ANALYSIS_OPENSWATH_MRMDECOY_H

#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.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 <boost/unordered_map.hpp>

#include <string>
#include <vector>
#include <map>
#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,
                        double mz_shift, bool exclude_similar,
                        double similarity_threshold, bool remove_CNterm_mods,
                        double precursor_mass_shift, std::vector<String> fragment_types,
                        std::vector<size_t> fragment_charges, bool enable_specific_losses,
                        bool enable_unspecific_losses, bool remove_unannotated,
                        int round_decPow = -4);

    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;

    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);

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

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

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

#endif