SpectrumAccessOpenMS.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMS_H
#define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMS_H

#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>

namespace OpenMS
{
  class OPENMS_DLLAPI SpectrumAccessOpenMS :
    public OpenSwath::ISpectrumAccess
  {
public:
    typedef OpenMS::MSExperiment<Peak1D> MSExperimentType;
    typedef OpenMS::MSSpectrum<Peak1D> MSSpectrumType;
    typedef OpenMS::MSChromatogram<ChromatogramPeak> MSChromatogramType;

    explicit SpectrumAccessOpenMS(MSExperimentType& ms_experiment);

    ~SpectrumAccessOpenMS();

    OpenSwath::SpectrumPtr getSpectrumById(int id) const;

    OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const;

    std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const;

    size_t getNrSpectra() const;

    SpectrumSettings getSpectraMetaInfo(int id) const;

    OpenSwath::ChromatogramPtr getChromatogramById(int id) const;

    // FEATURE ?
    // ChromatogramPtr getChromatogramByPrecursorMZ(double mz, double deltaMZ);

    size_t getNrChromatograms() const;

    ChromatogramSettings getChromatogramMetaInfo(int id) const;

    std::string getChromatogramNativeID(int id) const;

private:
    MSExperimentType* ms_experiment_;

  };
} //end namespace OpenMS

#endif