IndexedMzMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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"
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/INTERFACES/DataStructures.h>
#include <OpenMS/INTERFACES/ISpectrumAccess.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>

#include <string>
#include <fstream>

namespace OpenMS
{

namespace Internal
{

  class OPENMS_DLLAPI IndexedMzMLHandler
  {
      String filename_;
      std::vector< std::pair<std::string, std::streampos> > spectra_offsets_;
      std::vector< std::pair<std::string, std::streampos> > chromatograms_offsets_;
      std::streampos index_offset_;
      bool spectra_before_chroms_;
      std::ifstream filestream_;
      bool parsing_success_;
      bool skip_xml_checks_;

    void parseFooter_(String filename);

    std::string getChromatogramById_helper_(int id);

    std::string getSpectrumById_helper_(int id);

    public:

    IndexedMzMLHandler();

    explicit IndexedMzMLHandler(const String& filename);

    IndexedMzMLHandler(const IndexedMzMLHandler& source);

    ~IndexedMzMLHandler();

    void openFile(String filename);

    bool getParsingSuccess() const;

    size_t getNrSpectra() const;

    size_t getNrChromatograms() const;

    OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id);

    const OpenMS::MSSpectrum getMSSpectrumById(int id);

    void getMSSpectrumById(int id, OpenMS::MSSpectrum& s);

    OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id);

    const OpenMS::MSChromatogram getMSChromatogramById(int id);

    void getMSChromatogramById(int id, OpenMS::MSChromatogram& c);

    void setSkipXMLChecks(bool skip)
    {
      skip_xml_checks_ = skip;
    }

  };
}
}