How to use

IndexElement

in

uk.ac.ebi.pride.tools.jmzreader.model

accessFile.seek(indexElement.getStart());
int size = indexElement.getSize();

file.seek(indexElement.getStart());
byte[] buffer = new byte[indexElement.getSize()];
file.read(buffer);

inputFile.seek(indexElement.getStart());
byte[] bytes = new byte[indexElement.getSize()];
inputFile.read(bytes);
String spectrum = new String(bytes);

byte[] byteBuffer = new byte[indexElement.getSize()];
accFile.seek(indexElement.getStart());
accFile.read(byteBuffer);
String ms2Buffer = new String(byteBuffer);

public static Spectrum getIndexedSpectrum(File sourcefile, uk.ac.ebi.pride.tools.jmzreader.model.IndexElement indexElement) throws JMzReaderException {
  RandomAccessFile access = null;
  try {
    // read the XML from the file
    access = new RandomAccessFile(sourcefile, "r");
    // create the byte buffer
    byte[] bytes = new byte[indexElement.getSize()];
    // move to the position in the file
    access.seek(indexElement.getStart());
    // read the snipplet
    access.read(bytes);
    // create and return the string
    String snipplet = new String(bytes);
    MzXMLUnmarshaller localUnmarshaller = MzXMLUnmarshallerFactory.getInstance().initializeUnmarshaller();
    Scan scan = localUnmarshaller.unmarshal(snipplet, MzXmlElement.SCAN_LEVEL1);
    return new MzXMLSpectrum(scan);
  } catch (Exception e) {
    throw new JMzReaderException("Failed to read from mzXML file.", e);
  } finally {
    if (access != null) {
      try {
        access.close();
      } catch (IOException e) {
        // ignore
      }
    }
  }
}

byte[] buffer = new byte[indexElement.getSize()];
accessFile.seek(indexElement.getStart());
accessFile.read(buffer);