openms/include/OpenMS/INTERFACES/ISpectrumAccess.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/INTERFACES/DataStructures.h>
 
#include <vector>
#include <string>
#include <boost/shared_ptr.hpp>
 
namespace OpenMS
{
namespace Interfaces
{
 
  class OPENMS_DLLAPI ISpectraReader
  {
public:
    virtual ~ISpectraReader() {}
    virtual SpectrumPtr getSpectrumById(int id) const = 0;
    virtual SpectrumPtr getSpectrumById(const std::string& id) const = 0;
    virtual std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const = 0;
    virtual size_t getNrSpectra() const = 0;
    virtual SpectrumMetaPtr getSpectrumMetaById(int id) const = 0;
 
    /*
     * Do we need an Iterator here?
     * We would have to provide our own iterator wrapper class because we don't
     * know whether all the spectra are loaded at any given timepoint
    typedef SpectrumPtr const ConstSpectraIterator;
    ConstSpectraIterator beginSpectra() const;
    ConstSpectraIterator endSpectra() const;
    */
  };
  typedef boost::shared_ptr<ISpectraReader> SpectraReaderPtr;
 
 
  class OPENMS_DLLAPI IChromatogramsReader
  {
public:
    virtual ~IChromatogramsReader() {}
    virtual ChromatogramPtr getChromatogramById(int id) const = 0;
    virtual ChromatogramPtr getChromatogramById(const std::string& id) const = 0;
    virtual std::vector<std::size_t> getChromatogramByPrecursorMZ(double mz, double deltaMZ) const = 0;
    virtual std::size_t getNrChromatograms() const = 0;
    virtual ChromatogramMetaPtr getChromatogramMetaById(int id) const = 0;
 
    /*
     * Do we need an Iterator here?
     * We would have to provide our own iterator wrapper class because we don't
     * know whether all the chromatograms are loaded at any given timepoint
    ConstChromatogramIterator beginChromatograms() const;
    ConstChromatogramIterator endChromatograms() const;
    */
  };
  typedef boost::shared_ptr<IChromatogramsReader> ChromatogramsReaderPtr;
 
 
  class OPENMS_DLLAPI ISpectraWriter
  {
public:
    virtual ~ISpectraWriter() {}
    virtual void appendSpectrum(SpectrumPtr spectrum, bool write_through=false) = 0;
    virtual void flush() = 0;
  };
  typedef boost::shared_ptr<ISpectraWriter> SpectraWriterPtr;
 
 
  class OPENMS_DLLAPI IChromatogramsWriter
  {
public:
    virtual ~IChromatogramsWriter() {}
    virtual void appendChromatogram(ChromatogramPtr chromatogram, bool write_through=false) = 0;
    virtual void flush() = 0;
  };
  typedef boost::shared_ptr<IChromatogramsWriter> ChromatogramsWriterPtr;
 
} //end namespace Interfaces
} //end namespace OpenMS