SpectrumAccessSqMass.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/FORMAT/HANDLERS/MzMLSqliteHandler.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 SpectrumAccessSqMass :
    public OpenSwath::ISpectrumAccess
  {

public:
    typedef OpenMS::MSSpectrum MSSpectrumType;
    typedef OpenMS::MSChromatogram MSChromatogramType;

    SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler);

    SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler, const std::vector<int> & indices);

    SpectrumAccessSqMass(const SpectrumAccessSqMass& sp, const std::vector<int>& indices);

    ~SpectrumAccessSqMass() override;

    SpectrumAccessSqMass(const SpectrumAccessSqMass & rhs);

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

    OpenSwath::SpectrumPtr getSpectrumById(int /* id */) override;

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

    void getAllSpectra(std::vector< OpenSwath::SpectrumPtr > & spectra, std::vector< OpenSwath::SpectrumMeta > & spectra_meta) const;

    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:

    OpenMS::Internal::MzMLSqliteHandler handler_;
    std::vector<int> sidx_;
  };
} //end namespace OpenMS