private static IPeakSet<? extends IPeak> parsePeakSet(Node parent) throws XmlParserException {
// retrieve all the properties
Vector<IPeak> peaks = new Vector<IPeak>();
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("peaks")) {
NodeList nodes2 = node.getChildNodes();
for (int nodeid2 = 0; nodeid2 < nodes2.getLength(); ++nodeid2) {
Node node2 = nodes2.item(nodeid2);
if (node2.getNodeType() != Node.ELEMENT_NODE) continue;
IPeak peak = parseIPeak(node2);
if (peak != null) peaks.add(peak);
}
}
}
// create the bugger
IPeakSet<IPeak> peakset = new IPeakSet<IPeak>(peaks);
parseIPeak(parent, peakset);
return peakset;
}
private static MeasurementInfo parseMeasurement(Node parent) throws XmlParserException {
String id = "";
String label = "";
String sampleid = "";
Vector<FileInfo> files = null;
Vector<ScanInfo> scans = null;
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("id")) id = element.getTextContent();
else if (element.getTagName().equals("label")) label = element.getTextContent();
else if (element.getTagName().equals("sampleid")) sampleid = element.getTextContent();
else if (element.getTagName().equals("scans")) scans = parseScans(node);
else if (element.getTagName().equals("files")) files = parseFiles(node);
}
MeasurementInfo measurement = new MeasurementInfo(Integer.parseInt(id), sampleid);
measurement.setLabel(label);
measurement.addFileInfos(files);
if (scans != null) measurement.addScanInfos(scans);
return measurement;
}
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 Header parseHeader(Node parent) throws XmlParserException {
Header header = new Header();
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;
try {
if (element.getTagName().equals("nrpeaks"))
header.setNrPeaks(Integer.parseInt(element.getTextContent()));
else if (element.getTagName().equals("date")) header.setDate(element.getTextContent());
else if (element.getTagName().equals("owner")) header.setOwner(element.getTextContent());
else if (element.getTagName().equals("description"))
header.setDescription(element.getTextContent());
else if (element.getTagName().equals("sets")) header.addSetInfos(parseSets(element));
else if (element.getTagName().equals("measurements"))
header.addMeasurementInfos(parseMeasurements(element));
else if (element.getTagName().equals("annotations")) {
Vector<Annotation> annotations = parseAnnotations(element);
if (annotations != null)
for (Annotation annotation : annotations) header.addAnnotation(annotation);
}
} catch (Exception e) {
throw new XmlParserException(
"Invalid value in header (" + element.getTagName() + "): '" + e.getMessage() + "'.");
}
}
return header;
}
private static Vector<Annotation> parseAnnotations(Node parent) throws XmlParserException {
Vector<Annotation> annotations = new Vector<Annotation>();
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("annotation")) {
String label = null, value = null, valuetype = null, unit = null;
NodeList annotation_nodes = element.getChildNodes();
for (int annotationid = 0; annotationid < annotation_nodes.getLength(); ++annotationid) {
Node annotation_node = annotation_nodes.item(annotationid);
if (annotation_node.getNodeType() != Node.ELEMENT_NODE) continue;
Element annotation_element = (Element) annotation_node;
if (annotation_element.getTagName().equals("label"))
label = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("value"))
value = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("valuetype"))
valuetype = annotation_element.getTextContent();
}
if (label == null || value == null || valuetype == null)
throw new XmlParserException("Annotation is missing either: label, value or valuetype");
Annotation annotation =
new Annotation(label, value, Annotation.ValueType.valueOf(valuetype));
annotation.setUnit(unit);
if (annotation.getValueType() == Annotation.ValueType.ONTOLOGY)
annotation.setOntologyRef(element.getAttribute("ontologyref"));
if (element.getAttribute("unit") != null) annotation.setUnit(element.getAttribute("unit"));
annotations.add(annotation);
}
}
return annotations;
}
private static void parseIPeak(Node parent, IPeak peak) throws XmlParserException {
// retrieve all the properties
int scan = -1;
double retentiontime = -1;
double mass = -1;
double intensity = -1;
int patternid = -1;
int measurementid = -1;
// String sha1 = null;
Vector<Annotation> annotations = null;
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("patternid"))
patternid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("measurementid"))
measurementid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
else if (element.getTagName().equals("scan"))
scan = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("mass"))
mass = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("intensity"))
intensity = Double.parseDouble(element.getTextContent());
// else if (element.getTagName().equals("sha1sum"))
// sha1 = element.getTextContent();
}
// check whether obligatory values are missing
if (mass == -1 || intensity == -1)
throw new XmlParserException("Mass and/or intensity information is missing for IPeak.");
peak.setScanID(scan);
peak.setRetentionTime(retentiontime);
peak.setMass(mass);
peak.setIntensity(intensity);
peak.setPatternID(patternid);
peak.setMeasurementID(measurementid);
if (annotations != null)
for (Annotation annotation : annotations) peak.addAnnotation(annotation);
// check whether
// if (sha1!=null && !sha1.equals(peak.sha1()))
// throw new XmlParserException("SHA1-sum for individual ipeak element does not match.");
}
private static Vector<FileInfo> parseFiles(Node parent) throws XmlParserException {
Vector<FileInfo> files = new Vector<FileInfo>();
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("file")) files.add(parseFile(node));
}
return files;
}
private static FileInfo parseFile(Node parent) throws XmlParserException {
String label = "";
String name = "";
String location = "";
Vector<Annotation> annotations = null;
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("label")) label = element.getTextContent();
else if (element.getTagName().equals("name")) name = element.getTextContent();
else if (element.getTagName().equals("location")) location = element.getTextContent();
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(node);
}
FileInfo file = new FileInfo(label, name, location);
if (annotations != null) file.addAnnotations(annotations);
return file;
}
private static ScanInfo parseScan(Node parent) throws XmlParserException {
double retentiontime = 0;
Polarity polarity = Polarity.NEUTRAL;
Vector<Annotation> annotations = null;
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("polarity"))
polarity = Polarity.valueOf(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
}
ScanInfo scan = new ScanInfo(retentiontime, polarity);
if (annotations != null) scan.addAnnotations(annotations);
return scan;
}
@SuppressWarnings("unchecked")
private static BackgroundIon<? extends Peak> parseBackgroundIon(Node parent)
throws XmlParserException {
// retrieve the separate peaks
PeakData<? extends Peak> peakdata = null;
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("peakdata")) {
peakdata = parsePeakData(element);
}
}
// create the bugger
BackgroundIon<? extends Peak> backgroundion = null;
if (peakdata.getFactory().getPeakClass().equals(Centroid.class))
backgroundion = new BackgroundIon<Centroid>((PeakData<Centroid>) peakdata);
parseIPeak(parent, backgroundion);
return backgroundion;
}
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;
}