MzMLSpectrumDecoder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry               
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FORMAT/Base64.h>
#include <OpenMS/INTERFACES/DataStructures.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>
 
#include <string>
#include <xercesc/dom/DOMNode.hpp>
 
#include <OpenMS/FORMAT/HANDLERS/MzMLHandlerHelper.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MzMLSpectrumDecoder
  {
  protected:
 
    bool skip_xml_checks_; 
      
    typedef Internal::MzMLHandlerHelper::BinaryData BinaryData;
 
    OpenMS::Interfaces::SpectrumPtr decodeBinaryDataSpectrum_(std::vector<BinaryData> & data) const;
 
    void decodeBinaryDataMSSpectrum_(std::vector<BinaryData>& data, OpenMS::MSSpectrum& s) const;
 
    void decodeBinaryDataMSChrom_(std::vector<BinaryData>& data, OpenMS::MSChromatogram& c) const;
 
    OpenMS::Interfaces::ChromatogramPtr decodeBinaryDataChrom_(std::vector<BinaryData> & data) const;
 
    void handleBinaryDataArray_(xercesc::DOMNode * indexListNode, std::vector<BinaryData>& data);
 
    std::string domParseString_(const std::string& in, std::vector<BinaryData>& data);
 
  public:
 
    explicit MzMLSpectrumDecoder(bool skip_xml_checks = false) :
      skip_xml_checks_(skip_xml_checks)
    {}
 
    void domParseSpectrum(const std::string& in, OpenMS::Interfaces::SpectrumPtr & sptr);
 
    void domParseSpectrum(const std::string& in, MSSpectrum& s);
 
    void domParseChromatogram(const std::string& in, MSChromatogram& c);
 
    void domParseChromatogram(const std::string& in, OpenMS::Interfaces::ChromatogramPtr & cptr);
 
    void setSkipXMLChecks(bool only);
  };
}