MzXMLHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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: Timo Sachsenberg $
// $Authors: Marc Sturm, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

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

namespace OpenMS
{
  class MetaInfoInterface;
  namespace Interfaces
  {
    class IMSDataConsumer;
  }

  namespace Internal
  {
    

    typedef PeakMap MapType;
    typedef MSSpectrum SpectrumType;

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

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

      ~MzXMLHandler() override {}

      LOADDETAIL getLoadDetail() const override;

      void setLoadDetail(const LOADDETAIL d) override;

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

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

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

      void writeTo(std::ostream& os) override;

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

      UInt getScanCount() const
      {
        return scan_count_;
      }

      void setMSDataConsumer(Interfaces::IMSDataConsumer * consumer)
      {
        consumer_ = consumer;
      }

protected:

      typedef MapType::PeakType PeakType;
      typedef MSSpectrum SpectrumType;

      MapType* exp_;
      const MapType* cexp_;

      PeakFileOptions options_;

      Int nesting_level_;

      struct SpectrumData
      {
        UInt peak_count_;
        String precision_;
        String compressionType_;
        String char_rest_;
        SpectrumType spectrum;
        bool skip_data;
      };

      std::vector< SpectrumData > spectrum_data_;

      bool skip_spectrum_;

      UInt spec_write_counter_;

      Interfaces::IMSDataConsumer* consumer_;

      UInt scan_count_;

      const ProgressLogger& logger_;


      inline bool writeAttributeIfExists_(std::ostream& os, const MetaInfoInterface& meta, const String& metakey, const String& attname);

      inline void writeUserParam_(std::ostream& os, const MetaInfoInterface& meta, int indent = 4, const String& tag = "nameValue");

      void doPopulateSpectraWithData_(SpectrumData & spectrum_data);

      void populateSpectraWithData_();

      std::vector< boost::shared_ptr< DataProcessing> > data_processing_;


private:
      MzXMLHandler();
      
      void init_();
    };

  } // namespace Internal

} // namespace OpenMS