Method domParseString_

src/openms/source/FORMAT/HANDLERS/MzMLSpectrumDecoder.cpp:525–584

  }

  std::string MzMLSpectrumDecoder::domParseString_(const std::string& in, std::vector<BinaryData>& data)
  {
    // PRECONDITON is below (since we first need to do XML parsing before validating)
    // initializer list of XMLCh (= usually some type that fits utf16) from ASCII chars
    static constexpr XMLCh id_tag[] = {'i','d', 0};
    static constexpr XMLCh default_array_length_tag[] = { 'd','e','f','a','u','l','t','A','r','r','a','y','L','e','n','g','t','h', 0};
    static constexpr XMLCh binary_data_array_tag[] = { 'b','i','n','a','r','y','D','a','t','a','A','r','r','a','y', 0};

    //-------------------------------------------------------------
    // Create parser from input string using MemBufInputSource
    //-------------------------------------------------------------
    xercesc::MemBufInputSource myxml_buf(reinterpret_cast<const unsigned char*>(in.c_str()), in.length(), "myxml (in memory)");
    std::unique_ptr<xercesc::XercesDOMParser> parser = std::make_unique<xercesc::XercesDOMParser>(); // make sure it is deleted even in case of exceptions
    parser->setDoNamespaces(false);
    parser->setDoSchema(false);
    parser->setLoadExternalDTD(false);
    parser->parse(myxml_buf);

    //-------------------------------------------------------------
    // Start parsing
    // see http://www.yolinux.com/TUTORIALS/XML-Xerces-C.html
    //-------------------------------------------------------------

    // no need to free this pointer - owned by the parent parser object
    xercesc::DOMDocument* doc =  parser->getDocument();
    // Get the top-level element (needs to be <spectrum> or <chromatogram>)
    xercesc::DOMElement* elementRoot = doc->getDocumentElement();
    if (!elementRoot)
    {
      throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, in, "No root element");
    }

    OPENMS_PRECONDITION(xercesc::XMLString::equals(elementRoot->getTagName(), CONST_XMLCH("spectrum")) || xercesc::XMLString::equals(elementRoot->getTagName(), CONST_XMLCH("chromatogram")),
          (String("The input needs to contain a <spectrum> or <chromatogram> tag as root element. Got instead '") +
          String(Internal::unique_xerces_ptr(xercesc::XMLString::transcode(elementRoot->getTagName())).get()) + String("'.")).c_str())

    // defaultArrayLength is a required attribute for the spectrum and the
    // chromatogram tag (but still check for it first to be safe).
    if (elementRoot->getAttributeNode(default_array_length_tag) == nullptr)
    {
      throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
          in, "Root element does not contain defaultArrayLength XML tag.");
    }
    int default_array_length = xercesc::XMLString::parseInt(elementRoot->getAttribute(default_array_length_tag));
    OpenMS::Internal::StringManager sm;
    std::string id = sm.convert(elementRoot->getAttribute(id_tag));

    // Extract the binaryDataArray elements (there may be multiple) and process them
    xercesc::DOMNodeList* li = elementRoot->getElementsByTagName(binary_data_array_tag);
    for (Size i = 0; i < li->getLength(); i++)
    {
      // Will append one single BinaryData object to data      
      handleBinaryDataArray_(li->item(i), data);
      
      // Set the size correctly (otherwise MzMLHandlerHelper complains).
      data.back().size = default_array_length;
    }