/**
* @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
* java.lang.String)
*/
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
if (canceled) throw new SAXException("Parsing canceled");
// <NAME>
if (qName.equals(PeakListElementName_2_3.PEAKLIST_NAME.getElementName())) {
name = getTextOfElement();
logger.info("Loading peak list: " + name);
peakListName = name;
}
// <PEAKLIST_DATE>
if (qName.equals(PeakListElementName_2_3.PEAKLIST_DATE.getElementName())) {
dateCreated = getTextOfElement();
}
// <QUANTITY>
if (qName.equals(PeakListElementName_2_3.QUANTITY.getElementName())) {
String text = getTextOfElement();
totalRows = Integer.parseInt(text);
}
// <RAW_FILE>
if (qName.equals(PeakListElementName_2_3.RAWFILE.getElementName())) {
rawDataFileID = getTextOfElement();
RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
if (dataFile == null) {
throw new SAXException(
"Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
}
currentPeakListDataFiles.add(dataFile);
}
// <SCAN_ID>
if (qName.equals(PeakListElementName_2_3.SCAN_ID.getElementName())) {
byte[] bytes = Base64.decodeToBytes(getTextOfElement());
// make a data input stream
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
scanNumbers = new int[numOfMZpeaks];
for (int i = 0; i < numOfMZpeaks; i++) {
try {
scanNumbers[i] = dataInputStream.readInt();
} catch (IOException ex) {
throw new SAXException(ex);
}
}
}
// <REPRESENTATIVE_SCAN>
if (qName.equals(PeakListElementName_2_3.REPRESENTATIVE_SCAN.getElementName())) {
representativeScan = Integer.valueOf(getTextOfElement());
}
// <FRAGMENT_SCAN>
if (qName.equals(PeakListElementName_2_3.FRAGMENT_SCAN.getElementName())) {
fragmentScan = Integer.valueOf(getTextOfElement());
}
// <MASS>
if (qName.equals(PeakListElementName_2_3.MZ.getElementName())) {
byte[] bytes = Base64.decodeToBytes(getTextOfElement());
// make a data input stream
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
masses = new double[numOfMZpeaks];
for (int i = 0; i < numOfMZpeaks; i++) {
try {
masses[i] = (double) dataInputStream.readFloat();
} catch (IOException ex) {
throw new SAXException(ex);
}
}
}
// <HEIGHT>
if (qName.equals(PeakListElementName_2_3.HEIGHT.getElementName())) {
byte[] bytes = Base64.decodeToBytes(getTextOfElement());
// make a data input stream
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
intensities = new double[numOfMZpeaks];
for (int i = 0; i < numOfMZpeaks; i++) {
try {
intensities[i] = (double) dataInputStream.readFloat();
} catch (IOException ex) {
throw new SAXException(ex);
}
}
}
// <PEAK>
if (qName.equals(PeakListElementName_2_3.PEAK.getElementName())) {
DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
Range peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);
if (dataFile == null)
throw new SAXException("Error in project: data file " + peakColumnID + " not found");
for (int i = 0; i < numOfMZpeaks; i++) {
Scan sc = dataFile.getScan(scanNumbers[i]);
double retentionTime = sc.getRetentionTime();
double mz = masses[i];
double intensity = intensities[i];
if ((peakRTRange == null) || (peakIntensityRange == null)) {
peakRTRange = new Range(retentionTime);
peakIntensityRange = new Range(intensity);
} else {
peakRTRange.extendRange(retentionTime);
peakIntensityRange.extendRange(intensity);
}
if (mz > 0.0) {
mzPeaks[i] = new SimpleDataPoint(mz, intensity);
if (peakMZRange == null) peakMZRange = new Range(mz);
else peakMZRange.extendRange(mz);
}
}
FeatureStatus status = FeatureStatus.valueOf(peakStatus);
SimpleFeature peak =
new SimpleFeature(
dataFile,
mass,
rt,
height,
area,
scanNumbers,
mzPeaks,
status,
representativeScan,
fragmentScan,
peakRTRange,
peakMZRange,
peakIntensityRange);
peak.setCharge(currentPeakCharge);
if (currentIsotopes.size() > 0) {
SimpleIsotopePattern newPattern =
new SimpleIsotopePattern(
currentIsotopes.toArray(new DataPoint[0]),
currentIsotopePatternStatus,
currentIsotopePatternDescription);
peak.setIsotopePattern(newPattern);
currentIsotopes.clear();
}
buildingRow.addPeak(dataFile, peak);
}
// <IDENTITY_PROPERTY>
if (qName.equals(PeakListElementName_2_3.IDPROPERTY.getElementName())) {
identityProperties.put(identityPropertyName, getTextOfElement());
}
// <PEAK_IDENTITY>
if (qName.equals(PeakListElementName_2_3.PEAK_IDENTITY.getElementName())) {
SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
buildingRow.addPeakIdentity(identity, preferred);
}
// <ROW>
if (qName.equals(PeakListElementName_2_3.ROW.getElementName())) {
buildingPeakList.addRow(buildingRow);
buildingRow = null;
parsedRows++;
}
// <ISOTOPE>
if (qName.equals(PeakListElementName_2_3.ISOTOPE.getElementName())) {
String text = getTextOfElement();
String items[] = text.split(":");
double mz = Double.valueOf(items[0]);
double intensity = Double.valueOf(items[1]);
DataPoint isotope = new SimpleDataPoint(mz, intensity);
currentIsotopes.add(isotope);
}
if (qName.equals(PeakListElementName_2_3.METHOD_NAME.getElementName())) {
String appliedMethod = getTextOfElement();
appliedMethods.add(appliedMethod);
}
if (qName.equals(PeakListElementName_2_3.METHOD_PARAMETERS.getElementName())) {
String appliedMethodParam = getTextOfElement();
appliedMethodParameters.add(appliedMethodParam);
}
}
/** @see Runnable#run() */
public void run() {
setStatus(TaskStatus.PROCESSING);
logger.info("Started chromatogram builder on " + dataFile);
scans = scanSelection.getMatchingScans(dataFile);
int allScanNumbers[] = scanSelection.getMatchingScanNumbers(dataFile);
totalScans = scans.length;
// Check if the scans are properly ordered by RT
double prevRT = Double.NEGATIVE_INFINITY;
for (Scan s : scans) {
if (s.getRetentionTime() < prevRT) {
setStatus(TaskStatus.ERROR);
final String msg =
"Retention time of scan #"
+ s.getScanNumber()
+ " is smaller then the retention time of the previous scan."
+ " Please make sure you only use scans with increasing retention times."
+ " You can restrict the scan numbers in the parameters, or you can use the Crop filter module";
setErrorMessage(msg);
return;
}
prevRT = s.getRetentionTime();
}
// Create new peak list
newPeakList = new SimplePeakList(dataFile + " " + suffix, dataFile);
Chromatogram[] chromatograms;
HighestDataPointConnector massConnector =
new HighestDataPointConnector(
dataFile, allScanNumbers, minimumTimeSpan, minimumHeight, mzTolerance);
for (Scan scan : scans) {
if (isCanceled()) return;
MassList massList = scan.getMassList(massListName);
if (massList == null) {
setStatus(TaskStatus.ERROR);
setErrorMessage(
"Scan "
+ dataFile
+ " #"
+ scan.getScanNumber()
+ " does not have a mass list "
+ massListName);
return;
}
DataPoint mzValues[] = massList.getDataPoints();
if (mzValues == null) {
setStatus(TaskStatus.ERROR);
setErrorMessage(
"Mass list "
+ massListName
+ " does not contain m/z values for scan #"
+ scan.getScanNumber()
+ " of file "
+ dataFile);
return;
}
massConnector.addScan(scan.getScanNumber(), mzValues);
processedScans++;
}
chromatograms = massConnector.finishChromatograms();
// Sort the final chromatograms by m/z
Arrays.sort(chromatograms, new PeakSorter(SortingProperty.MZ, SortingDirection.Ascending));
// Add the chromatograms to the new peak list
for (Feature finishedPeak : chromatograms) {
SimplePeakListRow newRow = new SimplePeakListRow(newPeakID);
newPeakID++;
newRow.addPeak(dataFile, finishedPeak);
newPeakList.addRow(newRow);
}
// Add new peaklist to the project
project.addPeakList(newPeakList);
// Add quality parameters to peaks
QualityParameters.calculateQualityParameters(newPeakList);
setStatus(TaskStatus.FINISHED);
logger.info("Finished chromatogram builder on " + dataFile);
}
/**
* @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String,
* java.lang.String, org.xml.sax.Attributes)
*/
public void startElement(String namespaceURI, String lName, String qName, Attributes attrs)
throws SAXException {
if (canceled) throw new SAXException("Parsing canceled");
// <ROW>
if (qName.equals(PeakListElementName_2_3.ROW.getElementName())) {
if (buildingPeakList == null) {
initializePeakList();
}
int rowID = Integer.parseInt(attrs.getValue(PeakListElementName_2_3.ID.getElementName()));
buildingRow = new SimplePeakListRow(rowID);
String comment = attrs.getValue(PeakListElementName_2_3.COMMENT.getElementName());
buildingRow.setComment(comment);
}
// <PEAK_IDENTITY>
if (qName.equals(PeakListElementName_2_3.PEAK_IDENTITY.getElementName())) {
identityProperties = new Hashtable<String, String>();
preferred =
Boolean.parseBoolean(attrs.getValue(PeakListElementName_2_3.PREFERRED.getElementName()));
}
// <IDENTITY_PROPERTY>
if (qName.equals(PeakListElementName_2_3.IDPROPERTY.getElementName())) {
identityPropertyName = attrs.getValue(PeakListElementName_2_3.NAME.getElementName());
}
// <PEAK>
if (qName.equals(PeakListElementName_2_3.PEAK.getElementName())) {
peakColumnID = attrs.getValue(PeakListElementName_2_3.COLUMN.getElementName());
mass = Double.parseDouble(attrs.getValue(PeakListElementName_2_3.MZ.getElementName()));
// Before MZmine 2.6 retention time was saved in seconds, but now we
// use minutes, so we need to divide by 60
rt = Double.parseDouble(attrs.getValue(PeakListElementName_2_3.RT.getElementName())) / 60d;
height = Double.parseDouble(attrs.getValue(PeakListElementName_2_3.HEIGHT.getElementName()));
area = Double.parseDouble(attrs.getValue(PeakListElementName_2_3.AREA.getElementName()));
peakStatus = attrs.getValue(PeakListElementName_2_3.STATUS.getElementName());
String chargeString = attrs.getValue(PeakListElementName_2_3.CHARGE.getElementName());
if (chargeString != null) currentPeakCharge = Integer.valueOf(chargeString);
else currentPeakCharge = 0;
}
// <MZPEAK>
if (qName.equals(PeakListElementName_2_3.MZPEAKS.getElementName())) {
numOfMZpeaks =
Integer.parseInt(attrs.getValue(PeakListElementName_2_3.QUANTITY.getElementName()));
}
// <ISOTOPE_PATTERN>
if (qName.equals(PeakListElementName_2_3.ISOTOPE_PATTERN.getElementName())) {
currentIsotopes.clear();
currentIsotopePatternStatus =
IsotopePatternStatus.valueOf(
attrs.getValue(PeakListElementName_2_3.STATUS.getElementName()));
currentIsotopePatternDescription =
attrs.getValue(PeakListElementName_2_3.DESCRIPTION.getElementName());
}
}
