Method readMzIdentMLFile

src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp:134–303

* reads a mzid file into handlers pro_id_ & pep_id_ members */

     * reads a mzid file into handlers pro_id_ & pep_id_ members
     */
    void MzIdentMLDOMHandler::readMzIdentMLFile(const std::string& mzid_file)
    {
      // Test to see if the file is ok.
      struct stat fileStatus;

      errno = 0;
      if (stat(mzid_file.c_str(), &fileStatus) == -1) // ==0 ok; ==-1 error
      {
        if (errno == ENOENT) // errno declared by include file errno.h
        {
          throw (runtime_error("Path file_name does not exist, or path is an empty string."));
        }
        else if (errno == ENOTDIR)
        {
          throw (runtime_error("A component of the path is not a directory."));
        }
        // On MSVC 2008, the ELOOP constant is not declared and thus introduces a compile error
        //else if (errno == ELOOP)
        //  throw (runtime_error("Too many symbolic links encountered while traversing the path."));
        else if (errno == EACCES)
        {
          throw (runtime_error("Permission denied."));
        }
        else if (errno == ENAMETOOLONG)
        {
          throw (runtime_error("File can not be read."));
        }
      }

      // Configure DOM parser.
      mzid_parser_.setValidationScheme(XercesDOMParser::Val_Never);
      mzid_parser_.setDoNamespaces(false);
      mzid_parser_.setDoSchema(false);
      mzid_parser_.setLoadExternalDTD(false);

      try
      {
        mzid_parser_.parse(mzid_file.c_str());
      }
      catch (xercesc::XMLException& e)
      {
        char* message = xercesc::XMLString::transcode(e.getMessage());
        //          ostringstream errBuf;
        //          errBuf << "Error parsing file: " << message << flush;
        OPENMS_LOG_ERROR << "XERCES error parsing file: " << message << flush << endl;
        XMLString::release(&message);
      }

      // we adopt/own the document so we can free it in case this DOMHandler is reused on another file.
      xercesc::DOMDocument* xmlDoc = mzid_parser_.adoptDocument();

      try
      {
        // Catch special case: Cross-Linking MS
        DOMNodeList* additionalSearchParams = xmlDoc->getElementsByTagName(CONST_XMLCH("AdditionalSearchParams"));
        const  XMLSize_t as_node_count = additionalSearchParams->getLength();

        for (XMLSize_t i = 0; i < as_node_count; ++i)