MRMIonSeries.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <unordered_map>
 
// #define DEBUG_MRMIONSERIES
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MRMIonSeries
  {
private:
    TargetedExperiment::Interpretation annotationToCVTermList_(const String& annotation);
 
    void annotationToCV_(ReactionMonitoringTransition& tr);
 
public:
    MRMIonSeries();
 
    ~MRMIonSeries();
 
    typedef std::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);
  };
}