openms/include/OpenMS/INTERFACES/ISpectrumAccess.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $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