MzDataHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
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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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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_HANDLERS_MZDATAHANDLER_H
#define OPENMS_FORMAT_HANDLERS_MZDATAHANDLER_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/Base64.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <sstream>

namespace OpenMS
{
  namespace Internal
  {
  typedef PeakMap MapType;
  typedef MSSpectrum SpectrumType;
  typedef MSChromatogram ChromatogramType;

    class OPENMS_DLLAPI MzDataHandler :
      public XMLHandler
    {
public:
      MzDataHandler(MapType & exp, const String & filename, const String & version, ProgressLogger & logger);

      MzDataHandler(const MapType & exp, const String & filename, const String & version, const ProgressLogger & logger);

      virtual ~MzDataHandler()
      {
      }



      // Docu in base class
      virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);

      // Docu in base class
      virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);

      // Docu in base class
      virtual void characters(const XMLCh * const chars, const XMLSize_t length);

      void writeTo(std::ostream & os);

      void setOptions(const PeakFileOptions & options)
      {
        options_ = options;
      }

private:
      void init_();

protected:

      typedef MapType::PeakType PeakType;
      typedef MSSpectrum SpectrumType;

      MapType * exp_;
      const MapType * cexp_;

      PeakFileOptions options_;

      UInt peak_count_;
      SpectrumType spec_;
      std::vector<std::pair<String, MetaInfoDescription> > meta_id_descs_;
      std::vector<String> data_to_decode_;
      std::vector<float> data_to_encode_;
      std::vector<std::vector<float> > decoded_list_;
      std::vector<std::vector<double> > decoded_double_list_;
      std::vector<String> precisions_;
      std::vector<String> endians_;

      Base64 decoder_;

      bool skip_spectrum_;

      const ProgressLogger & logger_;

      void fillData_();



      inline void writeCVS_(std::ostream & os, double value, const String & acc, const String & name, UInt indent = 4) const;

      inline void writeCVS_(std::ostream & os, const String & value, const String & acc, const String & name, UInt indent = 4) const;

      inline void writeCVS_(std::ostream & os, UInt value, UInt map, const String & acc, const String & name, UInt indent = 4);

      inline void writeUserParam_(std::ostream & os, const MetaInfoInterface & meta, UInt indent = 4);

      void cvParam_(const String & name, const String & value);

      inline void writeBinary_(std::ostream & os, Size size, const String & tag, const String & name = "", SignedSize id = -1);

      //Data processing auxiliary variable
      boost::shared_ptr< DataProcessing > data_processing_;

    };

    //--------------------------------------------------------------------------------
  }   // namespace Internal

} // namespace OpenMS

#endif