IndexedMzMLFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#ifndef OPENMS_FORMAT_INDEXEDMZMLFILE_H
#define OPENMS_FORMAT_INDEXEDMZMLFILE_H

#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 <string>
#include <fstream>

namespace OpenMS
{

  class OPENMS_DLLAPI IndexedMzMLFile
  {
      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);

    public:

    IndexedMzMLFile();

    explicit IndexedMzMLFile(String filename);

    IndexedMzMLFile(const IndexedMzMLFile & source);

    ~IndexedMzMLFile();

    void openFile(String filename);

    bool getParsingSuccess() const;

    size_t getNrSpectra() const;

    size_t getNrChromatograms() const;

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

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

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

  };
}

#endif // OPENMS_FORMAT_INDEXEDMZMLFILE_H