SpectrumAccessOpenMS.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>

#include <boost/shared_ptr.hpp>

namespace OpenMS
{
  class OPENMS_DLLAPI SpectrumAccessOpenMS :
    public OpenSwath::ISpectrumAccess
  {
public:
    typedef OpenMS::PeakMap MSExperimentType;
    typedef OpenMS::MSSpectrum MSSpectrumType;
    typedef OpenMS::MSChromatogram MSChromatogramType;

    explicit SpectrumAccessOpenMS(boost::shared_ptr<MSExperimentType> ms_experiment);

    ~SpectrumAccessOpenMS() override;

    SpectrumAccessOpenMS(const SpectrumAccessOpenMS & rhs);

    boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;

    OpenSwath::SpectrumPtr getSpectrumById(int id) override;

    OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override;

    std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;

    size_t getNrSpectra() const override;

    SpectrumSettings getSpectraMetaInfo(int id) const;

    OpenSwath::ChromatogramPtr getChromatogramById(int id) override;

    // FEATURE ?
    // ChromatogramPtr getChromatogramByPrecursorMZ(double mz, double deltaMZ);

    size_t getNrChromatograms() const override;

    ChromatogramSettings getChromatogramMetaInfo(int id) const;

    std::string getChromatogramNativeID(int id) const override;

private:
    boost::shared_ptr<MSExperimentType> ms_experiment_;

  };
} //end namespace OpenMS