private static SetInfo parseSet(Node parent) throws XmlParserException {
String id = "";
String type = "";
String measurementids = null;
NodeList nodes = parent.getChildNodes();
Vector<SetInfo> sets = new Vector<SetInfo>();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("id")) id = element.getTextContent();
else if (element.getTagName().equals("set")) sets.add(parseSet(element));
else if (element.getTagName().equals("type")) type = element.getTextContent();
else if (element.getTagName().equals("measurementids"))
measurementids = element.getTextContent();
}
// create the set
SetInfo set = new SetInfo(id, Integer.parseInt(type));
if (measurementids != null) {
int mids[] = ByteArray.toIntArray(Base64.decode(measurementids), ByteArray.ENDIAN_LITTLE, 32);
for (int mid : mids) set.addMeasurementID(mid);
}
// add the children
for (SetInfo s : sets) set.addChild(s);
return set;
}
private static PeakData<? extends Peak> parsePeakData(Node parent) throws XmlParserException {
// get the attributes
Node typeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null) throw new XmlParserException("Failed to locate a type attribute.");
Node sizeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.SIZE);
if (sizeattribute == null) throw new XmlParserException("Failed to locate a size attribute.");
int size = Integer.parseInt(sizeattribute.getNodeValue());
String type = typeattribute.getNodeValue();
// create the arrays
int scanids[] = null;
int patternids[] = null;
int measurementids[] = null;
double masses[] = null;
double intensities[] = null;
double retentiontimes[] = null;
// retrieve all the data
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("scanids"))
scanids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("patternids"))
patternids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("measurementids"))
measurementids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("masses"))
masses =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("intensities"))
intensities =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("retentiontimes"))
retentiontimes =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
}
// create the PeakData instance
if (type.equals("centroid"))
return new PeakData<Centroid>(
Centroid.factory,
size,
scanids,
patternids,
measurementids,
masses,
intensities,
retentiontimes);
return null;
}
