SpectrumAccessOpenMSCached.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 2002-2017.
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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 <fstream>

namespace OpenMS
{

  class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
    public OpenSwath::ISpectrumAccess
  {

public:
    typedef OpenMS::PeakMap MSExperimentType;
    typedef OpenMS::MSSpectrum MSSpectrumType;

    explicit SpectrumAccessOpenMSCached(String filename);

    ~SpectrumAccessOpenMSCached() override;

    SpectrumAccessOpenMSCached(const SpectrumAccessOpenMSCached & 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;

    size_t getNrChromatograms() const override;

    ChromatogramSettings getChromatogramMetaInfo(int id) const;

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

private:

    MSExperimentType meta_ms_experiment_;

    std::ifstream ifs_;

    String filename_;

    String filename_cached_;

    std::vector<std::streampos> spectra_index_;
    std::vector<std::streampos> chrom_index_;
  };

} //end namespace