MzXMLHandler.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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/StringUtils.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 std::string& filename, const std::string& version, ProgressLogger& logger);
 
      MzXMLHandler(const MapType& exp, const std::string& filename, const std::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_;
        std::string precision_;
        std::string compressionType_;
        std::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 std::string& metakey, const std::string& attname);
 
      inline void writeUserParam_(std::ostream& os, const MetaInfoInterface& meta, int indent = 4, const std::string& tag = "nameValue");
 
      void doPopulateSpectraWithData_(SpectrumData & spectrum_data);
 
      void populateSpectraWithData_();
 
      std::vector< std::shared_ptr< DataProcessing> > data_processing_;
 
 
private:
      MzXMLHandler();
      
      void init_();
    };
 
  } // namespace Internal
 
} // namespace OpenMS