text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2017.
  //
  // 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.
  // --------------------------------------------------------------------------
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
  // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
  // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  //
  // --------------------------------------------------------------------------
  // $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 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() override;
  
      /// Copy constructor
      SpectrumAccessOpenMSCached(const SpectrumAccessOpenMSCached & rhs);
  
      /// Light clone operator (actual data will not get copied)
      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;
  
      size_t getNrChromatograms() const override;
  
      ChromatogramSettings getChromatogramMetaInfo(int id) const;
  
      std::string getChromatogramNativeID(int id) const override;
  
  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
  