SpectrumAccessOpenMSInMemory.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// 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 $
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#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>
#include <algorithm>    // std::lower_bound, std::upper_bound, std::sort

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

    explicit SpectrumAccessOpenMSInMemory(OpenSwath::ISpectrumAccess & origin);

    ~SpectrumAccessOpenMSInMemory() override;

    SpectrumAccessOpenMSInMemory(const SpectrumAccessOpenMSInMemory & 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;

    OpenSwath::ChromatogramPtr getChromatogramById(int id) override;

    size_t getNrChromatograms() const override;

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

private:

    std::vector< OpenSwath::SpectrumPtr > spectra_;
    std::vector< OpenSwath::SpectrumMeta > spectra_meta_;

    std::vector< OpenSwath::ChromatogramPtr > chromatograms_;
    std::vector< std::string > chromatogram_ids_;

  };

} //end namespace OpenMS