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 2002-2020.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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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