Method parseOffsets

src/openms/source/FORMAT/HANDLERS/IndexedMzMLDecoder.cpp:66–122

  }

  int IndexedMzMLDecoder::parseOffsets(const String& filename, std::streampos indexoffset, OffsetVector& spectra_offsets, OffsetVector& chromatograms_offsets)
  {
    //-------------------------------------------------------------
    // Open file, jump to end and read last indexoffset bytes into buffer.
    //-------------------------------------------------------------
    std::ifstream f(filename.c_str());
    if (!f.is_open())
    {
      throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
    }

    // get length of file:
    f.seekg(0, f.end);
    std::streampos length = f.tellg();

    if (indexoffset < 0 || indexoffset > length)
    {
      std::cerr << "IndexedMzMLDecoder::parseOffsets Error: Offset was " <<
        indexoffset << " (not between 0 and " << length << ")." << std::endl;
      return -1;
    }

    //-------------------------------------------------------------
    // Read full end of file to parse offsets for spectra and chroms
    //-------------------------------------------------------------
    // read data as a block into a buffer

    // allocate enough memory in buffer (+1 for string termination)
    std::streampos readl = length - indexoffset;
    char* buffer = new(std::nothrow) char[readl + std::streampos(1)];

    // catch case where not enough memory is available
    if (buffer == nullptr)
    {
      // Warning: Index takes up more than 10 % of the whole file, please check your input file." << std::endl;
      std::cerr << "IndexedMzMLDecoder::parseOffsets Could not allocate enough memory to read in index of indexedMzML" << std::endl; 
      std::cerr << "IndexedMzMLDecoder::parseOffsets calculated index offset " << indexoffset << " and file length " << length << 
        ", consequently tried to read into memory " << readl << " bytes." << std::endl;
      return -1;
    }

    // read into memory
    f.seekg(-readl, f.end);
    f.read(buffer, readl);
    buffer[readl] = '\0';

    //-------------------------------------------------------------
    // Add a sane start element and then give it to a DOM parser
    //-------------------------------------------------------------
    // http://stackoverflow.com/questions/4691039/making-xerces-parse-a-string-insted-of-a-file
    std::string tmp_fixed_xml = "<indexedmzML>" +  String(buffer) + "\n";
    int res = domParseIndexedEnd_(tmp_fixed_xml, spectra_offsets, chromatograms_offsets);

    delete[] buffer;

    return res;
  }