/* (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);
}
}
/**
* Helper to handle metadata in the document
*
* @throws CheckedIOException
*/
private void writeMetaData(PeakList peaklist) {
// skip if previously done
if (hasWrittenMetaData) {
return;
}
// flag meta-data as writter
hasWrittenMetaData = true;
// try to get meta-data if it is available
if (peaklist instanceof MzXMLPeakList) {
MzXMLPeakList mzxml = (MzXMLPeakList) peaklist;
msRun = mzxml.getMsRun();
} else {
msRun = new MsRun();
}
try {
// write out all the parent files
for (ParentFile pf : msRun.getParentFiles()) {
xmlw.writeEmptyElement("parentFile");
writeNonNull(xmlw, "fileName", pf.getFileName());
writeNonNull(xmlw, "fileType", pf.getFileType());
writeNonNull(xmlw, "fileSha1", pf.getFileSHA());
}
// write out all the msInstrument information
MsInstrument msInstrument = msRun.getMsInstrument();
if (msInstrument != null) {
xmlw.writeStartElement("msInstrument");
// write out msManufacture
if (msInstrument.getMsManufacturer() != null) {
xmlw.writeEmptyElement("msManufacturer");
writeNonNull(xmlw, "category", msInstrument.getMsManufacturer().getCategory());
if (msInstrument.getMsManufacturer().getValue() != null)
writeNonNull(xmlw, "value", msInstrument.getMsManufacturer().getValue());
}
// write out msModel
if (msInstrument.getMsModel() != null) {
xmlw.writeEmptyElement("msModel");
writeNonNull(xmlw, "category", msInstrument.getMsModel().getCategory());
writeNonNull(xmlw, "value", msInstrument.getMsModel().getValue());
}
// write out msManufacture
if (msInstrument.getMsIonisation() != null) {
xmlw.writeEmptyElement("msIonisation");
writeNonNull(xmlw, "category", msInstrument.getMsIonisation().getCategory());
writeNonNull(xmlw, "value", msInstrument.getMsIonisation().getValue());
}
// write out msManufacture
if (msInstrument.getMsMassAnalyzer() != null) {
xmlw.writeEmptyElement("msMassAnalyzer");
writeNonNull(xmlw, "category", msInstrument.getMsMassAnalyzer().getCategory());
writeNonNull(xmlw, "value", msInstrument.getMsMassAnalyzer().getValue());
}
// write out msManufacture
if (msInstrument.getMsDetector() != null) {
xmlw.writeEmptyElement("msDetector");
writeNonNull(xmlw, "category", msInstrument.getMsDetector().getCategory());
writeNonNull(xmlw, "value", msInstrument.getMsDetector().getValue());
}
// write out software
if (msInstrument.getSoftware() != null) {
xmlw.writeEmptyElement("software");
writeNonNull(xmlw, "type", msInstrument.getSoftware().getType());
writeNonNull(xmlw, "name", msInstrument.getSoftware().getName());
writeNonNull(xmlw, "version", msInstrument.getSoftware().getVersion());
writeNonNull(xmlw, "completionTime", msInstrument.getSoftware().getCompletionTime());
}
// write out msResolution
if (msInstrument.getMsResolution() != null) {
xmlw.writeEmptyElement("msResolution");
writeNonNull(xmlw, "category", msInstrument.getMsResolution().getCategory());
writeNonNull(xmlw, "value", msInstrument.getMsResolution().getValue());
}
// write out operator
if (msInstrument.getOperator() != null) {
xmlw.writeEmptyElement("operator");
writeNonNull(xmlw, "first", msInstrument.getOperator().getFirst());
writeNonNull(xmlw, "last", msInstrument.getOperator().getLast());
writeNonNull(xmlw, "email", msInstrument.getOperator().getEmail());
writeNonNull(xmlw, "phone", msInstrument.getOperator().getPhone());
writeNonNull(xmlw, "URI", msInstrument.getOperator().getURI());
}
xmlw.writeEndElement();
}
// write out all the dataProcessing information
for (DataProcessing dp : msRun.getDataProcessings()) {
xmlw.writeStartElement("dataProcessing");
writeNonNull(xmlw, "intensityCutoff", dp.getIntensityCutoff());
writeNonNull(xmlw, "centroided", dp.getCentroided());
writeNonNull(xmlw, "deisotoped", dp.getDeisotoped());
writeNonNull(xmlw, "chargeDeconvoluted", dp.getChargeDeconvoluted());
writeNonNull(xmlw, "spotIntegration", dp.getSpotIntegration());
// get all software
Software software = dp.getSoftware();
// write out software
if (software != null) {
xmlw.writeEmptyElement("software");
writeNonNull(xmlw, "type", software.getType());
writeNonNull(xmlw, "name", software.getName());
writeNonNull(xmlw, "version", software.getVersion());
writeNonNull(xmlw, "completionTime", software.getCompletionTime());
}
xmlw.writeEndElement();
}
} catch (XMLStreamException e) {
throw new RuntimeException("Can't write mzXML meta-data!", e);
}
}