MRMIonSeries.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 2002-2018.
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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger $
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#pragma once

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <boost/unordered_map.hpp>
#include <boost/assign.hpp>
#include <boost/lexical_cast.hpp>

// #define DEBUG_MRMIONSERIES

namespace OpenMS
{

  class OPENMS_DLLAPI MRMIonSeries
  {
private:
    TargetedExperiment::Interpretation annotationToCVTermList_(const String& annotation);

    void annotationToCV_(ReactionMonitoringTransition& tr);

public:
    MRMIonSeries();

    ~MRMIonSeries();

    typedef boost::unordered_map<String, double> IonSeries;

    std::pair<String, double> getIon(IonSeries& ionseries, const String& ionid);

    std::pair<String, double> annotateIon(const IonSeries& ionseries, const double ProductMZ, const double mz_threshold);

    void annotateTransitionCV(ReactionMonitoringTransition& tr, const String& annotation);

    void annotateTransition(ReactionMonitoringTransition& tr,
                            const TargetedExperiment::Peptide& peptide,
                            const double precursor_mz_threshold,
                            const double product_mz_threshold,
                            const bool enable_reannotation,
                            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);

    IonSeries getIonSeries(const AASequence& sequence,
                           size_t precursor_charge,
                           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);
  };
}