/**
* Lookup a Software product and return it or return a new one if not found.
*
* @param name the name of the software product to lookup
* @return a new or existing Software product associated with this Company
*/
public Software lookupOrCreateSoftware(String name) {
Software s = (Software) lnkSoftware.get(name);
if (s == null) {
s = new Software(name);
lnkSoftware.put(s.getName(), s);
}
return s;
}
/**
* 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);
}
}