MRMIonSeries.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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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_(String annotation);

    void annotationToCV_(ReactionMonitoringTransition& tr);

public:
    MRMIonSeries();

    ~MRMIonSeries();

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

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

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

    void annotateTransitionCV(ReactionMonitoringTransition& tr, String annotation);

    void annotateTransition(ReactionMonitoringTransition& tr, const TargetedExperiment::Peptide peptide, const double precursor_mz_threshold, const double product_mz_threshold, bool enable_reannotation, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow = -4);

    IonSeries getIonSeries(AASequence sequence, size_t precursor_charge, std::vector<String> fragment_types, std::vector<size_t> fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow = -4);
  };
}