MzMLFile.h

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

#ifndef OPENMS_FORMAT_MZMLFILE_H
#define OPENMS_FORMAT_MZMLFILE_H

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

namespace OpenMS
{
  class OPENMS_DLLAPI MzMLFile :
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    MzMLFile();
    ~MzMLFile();

    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::MzMLHandler<MapType> handler(map, filename, schema_version_, *this);
      handler.setOptions(options_);
      //handler can throw parse error and other errors - catch those here - they are the cause for a parse error - report accordingly
      try
      {
        parse_(filename, &handler);
      }
      catch (Exception::BaseException & e)
      {
        std::string expr;
        expr.append(e.getFile());
        expr.append("@");
        std::stringstream ss;
        ss << e.getLine();             // we need c++11!! maybe in 2012?
        expr.append(ss.str());
        expr.append("-");
        expr.append(e.getFunction());
        std::string mess = "- due to that error of type ";
        mess.append(e.getName());
        throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, expr, mess);
      }

    }

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

    bool isValid(const String & filename, std::ostream & os = std::cerr);

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

private:

    PeakFileOptions options_;

    String indexed_schema_location_;
  };

} // namespace OpenMS

#endif // OPENMS_FOMAT_MZMLFILE_H