MzDataFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_MZDATAFILE_H
#define OPENMS_FORMAT_MZDATAFILE_H

#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/HANDLERS/MzDataHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/DocumentIdentifier.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MzDataFile :
    public Internal::XMLFile,
    public ProgressLogger
  {

public:

    MzDataFile();
    ~MzDataFile();

    PeakFileOptions & getOptions();

    const PeakFileOptions & getOptions() const;

    template <typename MapType>
    void load(const String & filename, MapType & map)
    {
      map.reset();

      //set DocumentIdentifier
      map.setLoadedFileType(filename);
      map.setLoadedFilePath(filename);

      Internal::MzDataHandler<MapType> handler(map, filename, schema_version_, *this);
      handler.setOptions(options_);
      parse_(filename, &handler);
    }

    template <typename MapType>
    void store(const String & filename, const MapType & map) const
    {
      Internal::MzDataHandler<MapType> handler(map, filename, schema_version_, *this);
      handler.setOptions(options_);
      save_(filename, &handler);
    }

    bool isSemanticallyValid(const String & filename, StringList & errors, StringList & warnings);

private:

    PeakFileOptions options_;
  };

} // namespace OpenMS

#endif // OPENMS_FOMAT_MZXMLFILE_H