MRMChromHandler.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/KERNEL/MSChromatogram.h>
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
// Need ChromExtractParams (defined in OpenSwathWorkflow.h)
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
 
// LightTargetedExperiment is defined in OpenSwath (openswathalgo). Forward-declare here to avoid
// including a non-existent OpenMS header location.
namespace OpenSwath { struct LightTargetedExperiment; }
 
 
namespace OpenMS
{
class OPENMS_DLLAPI MRMChromHandler : public IChromatogramHandler
{
public:
  MRMChromHandler();
  ~MRMChromHandler() 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;
 
  static void normalizeChromatogramMZ(MSChromatogram& chrom);
 
};
 
} // namespace OpenMS