public void onDocument(Document document, String xpath) throws XmlParserException {
if (xpath.equals(XPATH_IPEAK)) {
Node node = document.getFirstChild();
// check whether we're getting the correct ipeak
Node typeattribute = node.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null)
throw new XmlParserException("Failed to locate the type attribute.");
if (!typeattribute.getNodeValue().equals(PeakMLWriter.TYPE_BACKGROUNDION))
throw new XmlParserException(
"IPeak ("
+ typeattribute.getNodeValue()
+ ") is not of type: '"
+ PeakMLWriter.TYPE_BACKGROUNDION
+ "'");
// parse this node as a mass chromatogram
BackgroundIon<? extends Peak> backgroundion = parseBackgroundIon(node);
if (backgroundion != null) peaks.add(backgroundion);
//
if (_listener != null && result.header != null && result.header.getNrPeaks() != 0)
_listener.update((100. * index++) / result.header.getNrPeaks());
} else if (xpath.equals(XPATH_HEADER)) {
result.header = parseHeader(document.getFirstChild());
}
}
private static IPeak parseIPeak(Node parent) throws XmlParserException {
Node type = parent.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (type == null) return null;
else if (type.getNodeValue().equals(PeakMLWriter.TYPE_PEAKSET)) return parsePeakSet(parent);
else if (type.getNodeValue().equals(PeakMLWriter.TYPE_BACKGROUNDION))
return parseBackgroundIon(parent);
else if (type.getNodeValue().equals(PeakMLWriter.TYPE_MASSCHROMATOGRAM))
return parseMassChromatogram(parent);
else return null;
}
public void onDocument(Document document, String xpath) throws XmlParserException {
if (xpath.equals(XPATH_IPEAK)) {
Node node = document.getChildNodes().item(0);
// check whether we're getting the correct ipeak
Node typeattribute = node.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null
|| !typeattribute.getNodeValue().equals(PeakMLWriter.TYPE_PEAKSET))
throw new XmlParserException("Failed to locate a type attribute.");
// parse this node as a mass chromatogram
IPeakSet<? extends IPeak> peakset = parsePeakSet(node);
if (peakset != null) peaks.add(peakset);
//
if (_listener != null && result.header != null && result.header.getNrPeaks() != 0)
_listener.update((100. * index++) / result.header.getNrPeaks());
} else if (xpath.equals(XPATH_HEADER)) {
result.header = parseHeader(document.getFirstChild());
}
}
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;
}
