MRMMapping.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
// Forward-declare LightTargetedExperiment from OpenSwath (openswathalgo)
namespace OpenSwath { struct LightTargetedExperiment; }
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MRMMapping :
    public DefaultParamHandler
  {
public:
 
    MRMMapping();
 
    ~MRMMapping() override {}
 
    void mapExperiment(const OpenMS::PeakMap& input_chromatograms,
        const OpenMS::TargetedExperiment& targeted_exp,
        OpenMS::PeakMap& output) const;
 
    void mapExperiment(const OpenMS::PeakMap& input_chromatograms,
      const OpenSwath::LightTargetedExperiment& targeted_exp,
      OpenMS::PeakMap& output) const;
 
protected:
 
    MRMMapping(const MRMMapping & rhs);
 
    MRMMapping & operator=(const MRMMapping & rhs);
 
    void updateMembers_() override;
 
    double precursor_tol_;
    double product_tol_;
    bool map_multiple_assays_;
    bool error_on_unmapped_;
 
  };
}