IChromatogramHandler.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/KERNEL/MSChromatogram.h>
 
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <memory>
 
// Forward-declare OpenSwath types at global namespace (defined in openswathalgo)
namespace OpenSwath { struct LightTargetedExperiment; struct SwathMap; }
 
namespace OpenMS
{
  // ChromExtractParams is defined in OpenSwathWorkflow.h (OpenMS namespace)
  struct ChromExtractParams;
 
  class OPENMS_DLLAPI IChromatogramHandler
  {
  public:
    IChromatogramHandler() = default;
    virtual ~IChromatogramHandler() = default;
 
    virtual 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) = 0;
 
    virtual std::vector<MSChromatogram> extractAndMapChromatogramsForTransitions(
      const std::vector< OpenSwath::SwathMap > & swath_maps,
      const OpenSwath::LightTargetedExperiment & transition_exp,
      const ChromExtractParams & cp,
      const Param & mrm_mapping_param) = 0;
 
    static std::unique_ptr<IChromatogramHandler> createDefault();
  };
 
} // namespace OpenMS