DefaultChromHandler.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: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
#pragma once
 
#include <OpenMS/ANALYSIS/TARGETED/IChromatogramHandler.h>
#include <OpenMS/ANALYSIS/TARGETED/MRMChromHandler.h>
#include <OpenMS/ANALYSIS/TARGETED/DIAChromHandler.h>
#include <memory>
 
namespace OpenMS
{
  class OPENMS_DLLAPI DefaultChromHandler : public IChromatogramHandler
  {
  public:
    DefaultChromHandler();
    ~DefaultChromHandler() override;
 
    std::vector<MSChromatogram> collectIrtChromatogramsForIrt(
      const std::vector< OpenSwath::SwathMap > & swath_maps,
      const OpenSwath::LightTargetedExperiment & irt_transitions,
      const Param & mrm_mapping_param,
      const ChromExtractParams & cp,
      const TransformationDescription& trafo = TransformationDescription(),
      bool pasef = false,
      bool load_into_memory = false) override;
 
    std::vector<MSChromatogram> extractAndMapChromatogramsForTransitions(
      const std::vector< OpenSwath::SwathMap > & swath_maps,
      const OpenSwath::LightTargetedExperiment & transition_exp,
      const ChromExtractParams & cp,
      const Param & mrm_mapping_param) override;
 
  private:
    std::unique_ptr<MRMChromHandler> mrm_;
    std::unique_ptr<DIAChromHandler> dia_;
  };
 
} // namespace OpenMS