/**
* Parse function for loading a PeakML file containing only masschromatogram entries. When an
* entry of another type is encountered an {@link XmlParserException} is thrown. The resulting
* {@link ParseResult} instance is type-bound to {@link MassChromatogram} to force only
* masschromatogram types.
*
* @param in The input-stream to load the data from.
* @return The header and peak information stored in the file.
* @throws IOException Thrown on an IOException.
* @throws XmlParserException Thrown when an unknown IPeak object is encountered.
*/
public static ParseResult parseMassChromatograms(InputStream in, ParserProgressListener listener)
throws IOException, XmlParserException {
final ParseResult result = new ParseResult();
final Vector<MassChromatogram<? extends Peak>> peaks =
new Vector<MassChromatogram<? extends Peak>>();
final ParserProgressListener _listener = listener;
class myListener implements XmlParserListener {
int index = 0;
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)
throw new XmlParserException("Failed to locate the type attribute.");
if (!typeattribute.getNodeValue().equals(PeakMLWriter.TYPE_MASSCHROMATOGRAM))
throw new XmlParserException(
"IPeak ("
+ typeattribute.getNodeValue()
+ ") is not of type: '"
+ PeakMLWriter.TYPE_MASSCHROMATOGRAM
+ "'");
// parse this node as a mass chromatogram
MassChromatogram<? extends Peak> masschromatogram = parseMassChromatogram(node);
if (masschromatogram != null) peaks.add(masschromatogram);
//
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());
}
}
}
run(in, new myListener());
result.measurement = new IPeakSet<MassChromatogram<? extends Peak>>(peaks);
return result;
}
/**
* Parse function for blindly loading data from a PeakML file. This method loads the data in a
* PeakML file as it encounters it in the file. This means that a mix-model is essentially
* possible for peak-data stored in a PeakML file. The resulting {@link ParseResult} instance is
* parameterized with {@link IPeak}. The class-information made available through the Java
* language can be used to determine the original type of the peak. The function employs a
* callback mechanism with {@link ParserProgressListener} to return information about the progress
* through the file. This is calculated with the information returned by {@link
* Header#getNrPeaks()}.
*
* <p>The loadall parameter can be used to restrict the amount of data actually being loaded by
* the function. If this is set to false only data known by the {@link IPeak} class is loaded (in
* this implementation this means that an instance of the {@link Centroid} is made). The class
* information cannot be used to determine the original type of the peak when loadall is set to
* false.
*
* @param in The input-stream to load the data from.
* @param listener The progress listener.
* @param loadall If set to false only the data known to IPeak is loaded as class Peak.
* @return The header and peak information stored in the file.
* @throws IOException Thrown on an IOException.
* @throws XmlParserException Thrown when an unknown IPeak object is encountered.
*/
public static ParseResult parse(InputStream in, ParserProgressListener listener, boolean loadall)
throws IOException, XmlParserException {
// final boolean _loadall = loadall;
final ParserProgressListener _listener = listener;
final ParseResult result = new ParseResult();
final Vector<IPeak> peaks = new Vector<IPeak>();
class myListener implements XmlParserListener {
int index = 0;
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)
throw new XmlParserException("Failed to locate a type attribute.");
// ...
// IPeak peak = (_loadall ? parseIPeak(node) : parseCentroid(node));
IPeak peak = parseIPeak(node);
if (peak != null) peaks.add(peak);
//
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());
}
}
}
run(in, new myListener());
result.measurement = new IPeakSet<IPeak>(peaks);
return result;
}