/** Test of filter method, of class org.proteomecommons.io.filter.IntensityPeakListFilter. */
public void testFilter() {
System.out.println("filter");
GenericPeakList peaklist = new GenericPeakList();
GenericPeak gpa = new GenericPeak();
GenericPeak gpb = new GenericPeak();
GenericPeak parent = new GenericPeak();
gpa.setIntensity(5);
gpa.setMassOverCharge(2);
gpb.setIntensity(1);
gpb.setMassOverCharge(1);
parent.setCharge(1);
parent.setIntensity(4);
parent.setMassOverCharge(5);
peaklist.setParentPeak(parent);
peaklist.setPeaks(new Peak[] {gpa, gpb});
IntensityPeakListFilter instance = new IntensityPeakListFilter(1);
PeakList res = instance.filter(peaklist);
assertEquals(res.getParentPeak().getIntensity(), parent.getIntensity());
assertEquals(res.getPeaks().length, 1);
assertEquals(res.getPeaks()[0].getIntensity(), gpa.getIntensity());
assertEquals(res.getPeaks()[0].getMassOverCharge(), gpa.getMassOverCharge());
}
/* (non-Javadoc)
* @see org.proteomecommons.io.PeakListWriter#startPeakList()
*/
public void write(PeakList pl) {
try {
// TODO Auto-generated method stub
if (!hasWrittenMetaData) {
writeMetaData(pl);
}
// write peak list
Peak[] peaks = pl.getPeaks();
// assume 32 bit for compatibility
int byteBufferCapacity = (32 / 8) * 2 * peaks.length;
// if 64 bit, recalc precision
if (!isUse32BitPrecision()) {
// bytes needed = (bits per double/bits per byte)*2 double per peak*number of peaks
byteBufferCapacity = (64 / 8) * 2 * peaks.length;
}
// make the buffer
ByteBuffer bb = ByteBuffer.allocate(byteBufferCapacity);
// network byte order is big endian http://mindprod.com/jgloss/endian.html
bb = bb.order(ByteOrder.BIG_ENDIAN);
// flatten the peaks into the buffer
for (int i = 0; i < peaks.length; i++) {
// dump the peak bytes into the buffer
Peak current = (Peak) peaks[i];
// assume 32 bit precision
if (isUse32BitPrecision()) {
bb.putFloat((float) current.getMassOverCharge());
bb.putFloat((float) current.getIntensity());
} else {
bb.putDouble(current.getMassOverCharge());
bb.putDouble(current.getIntensity());
}
}
// convert bytes
String encodedBytes = Base64.encodeBytes(bb.array(), false);
// finally, write out the xml
try {
// setup scan element
xmlw.writeStartElement("scan");
// write out a unique scan number to identify it
xmlw.writeAttribute("num", "" + scanNumber);
scanNumber++;
// write out the ms level
if (pl.getTandemCount() != PeakList.UNKNOWN_TANDEM_COUNT) {
xmlw.writeAttribute("msLevel", "" + pl.getTandemCount());
}
// number of peaks
xmlw.writeAttribute("peaksCount", "" + peaks.length);
// if it is an MZXMLPeakList write the other meta-data
if (pl instanceof MzXMLPeakList) {
MzXMLPeakList mzxmlpl = (MzXMLPeakList) pl;
writeNonNull(xmlw, "polarity", mzxmlpl.getPolarity());
writeNonNull(xmlw, "scanType", mzxmlpl.getScanType());
writeNonNull(xmlw, "centroided", mzxmlpl.getCentroided());
writeNonNull(xmlw, "deisotoped", mzxmlpl.getDeisotoped());
writeNonNull(xmlw, "chargeDeconvoluted", mzxmlpl.getChargeDeconvoluted());
writeNonNull(xmlw, "retentionTime", mzxmlpl.getRetentionTime());
writeNonNull(xmlw, "ionisationEnergy", mzxmlpl.getIonisationEnergy());
writeNonNull(xmlw, "collisionEnergy", mzxmlpl.getCollisionEnergy());
writeNonNull(xmlw, "startMz", mzxmlpl.getStartMz());
writeNonNull(xmlw, "endMz", mzxmlpl.getEndMz());
writeNonNull(xmlw, "lowMz", mzxmlpl.getLowMz());
writeNonNull(xmlw, "highMz", mzxmlpl.getHighMz());
writeNonNull(xmlw, "basePeakMz", mzxmlpl.getBasePeakMz());
writeNonNull(xmlw, "basePeakIntensity", mzxmlpl.getBasePeakIntensity());
writeNonNull(xmlw, "totIonCurrent", mzxmlpl.getTotIonCurrent());
}
// write precursor mz info
if (pl.getParentPeak() != null) {
Peak parentPeak = pl.getParentPeak();
if (parentPeak.getIntensity() == Peak.UNKNOWN_INTENSITY) {
throw new RuntimeException("mzXML requires an intensity value for precursor peaks.");
}
if (parentPeak.getMassOverCharge() == Peak.UNKNOWN_MZ) {
throw new RuntimeException("mzXML requires an mz value for precursor peaks.");
}
// close the precursorMz element
xmlw.writeStartElement("precursorMz");
writeNonNull(
xmlw, "precursorIntensity", Float.toString((float) parentPeak.getIntensity()));
if (parentPeak.getCharge() != Peak.UNKNOWN_CHARGE) {
xmlw.writeAttribute("precursorCharge", Integer.toString(parentPeak.getCharge()));
}
xmlw.writeCharacters(Float.toString((float) parentPeak.getMassOverCharge()));
// close the precursorMz element
xmlw.writeEndElement();
}
// setup peaks element
xmlw.writeStartElement("peaks");
if (isUse32BitPrecision()) {
xmlw.writeAttribute("precision", "32");
} else {
xmlw.writeAttribute("precision", "64");
}
// these two values are always the same
xmlw.writeAttribute("byteOrder", "network");
xmlw.writeAttribute("pairOrder", "m/z-int");
xmlw.writeCharacters(encodedBytes);
// end everything
xmlw.writeEndElement(); // peaks
xmlw.writeEndElement(); // scan
} catch (XMLStreamException e) {
throw new RuntimeException("Can't write peak list!", e);
}
} catch (Exception e) {
throw new RuntimeException("Can't write peak list!", e);
}
}