MetaboTargetedTargetDecoy.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: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
 
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MetaboTargetedTargetDecoy
  {
    public:
    class MetaboTargetDecoyMassMapping
    {
    public:
 
      String identifier; 
      String target_compound_ref; 
      String decoy_compound_ref; 
      std::vector<double> target_product_masses; 
      std::vector<double> decoy_product_masses; 
    };
 
    static std::vector<MetaboTargetDecoyMassMapping> constructTargetDecoyMassMapping(const TargetedExperiment& t_exp);
 
    static void resolveOverlappingTargetDecoyMassesByIndividualMassShift(TargetedExperiment& t_exp, std::vector<MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping>& mappings, const double& mass_to_add);
 
    static void generateMissingDecoysByMassShift(TargetedExperiment& t_exp, std::vector<MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping>& mappings, const double& mass_to_add);
 
  protected:
    static std::map<String, std::vector<OpenMS::ReactionMonitoringTransition> > constructTransitionsMap_(const TargetedExperiment& t_exp);
  };
 
} // namespace OpenMS