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 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * 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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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