SpectrumAccessOpenMSInMemory.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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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>
#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