// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMSCACHED_H
#define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMSCACHED_H

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

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

#include <fstream>

namespace OpenMS
{

  /**
    @brief An implementation of the Spectrum Access interface using on-disk caching

    This class implements the OpenSWATH Spectrum Access interface
    (ISpectrumAccess) using the CachedmzML class which is able to read and
    write a cached mzML file.

    @note This implementation is @a not thread-safe since it keeps internally a
    single file access pointer which it moves when accessing a specific
    data item. The caller is responsible to ensure that access is performed
    atomically.

  */
  class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
    public OpenSwath::ISpectrumAccess
  {

public:
    typedef OpenMS::PeakMap MSExperimentType;
    typedef OpenMS::MSSpectrum<Peak1D> MSSpectrumType;

    /**
      @brief Constructor, opens the file stream

      @param filename The filename of the .mzML file (it is assumed a second
      file .mzML.cached exists).

      @throws Exception::FileNotFound is thrown if the file is not found
      @throws Exception::ParseError is thrown if the file cannot be parsed
    */
    explicit SpectrumAccessOpenMSCached(String filename);

    /**
      @brief Destructor
    */
    ~SpectrumAccessOpenMSCached();

    /// Copy constructor
    SpectrumAccessOpenMSCached(const SpectrumAccessOpenMSCached & rhs);

    /// Light clone operator (actual data will not get copied)
    boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const;

    OpenSwath::SpectrumPtr getSpectrumById(int id);

    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);

    size_t getNrChromatograms() const;

    ChromatogramSettings getChromatogramMetaInfo(int id) const;

    std::string getChromatogramNativeID(int id) const;

private:

    /// Meta data
    MSExperimentType meta_ms_experiment_;

    /// Internal filestream 
    std::ifstream ifs_;

    /// Name of the mzML file
    String filename_;

    /// Name of the cached mzML file
    String filename_cached_;

    /// Indices
    std::vector<std::streampos> spectra_index_;
    std::vector<std::streampos> chrom_index_;
  };

} //end namespace

#endif
