MzMLSpectrumDecoder.h

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//                   OpenMS -- Open-Source Mass Spectrometry               
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#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);
  };
}