Examples with SimpleFeature net.sf.mzmine.datamodel.impl.SimpleFeature used on opensource projects

Example 26 with SimpleFeature

use of net.sf.mzmine.datamodel.impl.SimpleFeature in project mzmine2 by mzmine.

the class PeakListOpenHandler_2_0 method endElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
 *      java.lang.String)
 */
@Override
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // <NAME>
    if (qName.equals(PeakListElementName_2_0.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading feature list: " + name);
        peakListName = name;
    }
    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_0.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }
    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_0.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }
    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_0.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException("Cannot open feature list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }
    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_0.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_0.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }
    if (qName.equals(PeakListElementName_2_0.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }
    // <All_MS2_FRAGMENT_SCANS>
    if (qName.equals(PeakListElementName_2_5.ALL_MS2_FRAGMENT_SCANS.getElementName())) {
        Integer fragmentNumber = Integer.valueOf(getTextOfElement());
        currentAllMS2FragmentScans.add(fragmentNumber);
    }
    // <MASS>
    if (qName.equals(PeakListElementName_2_0.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] = dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }
    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_0.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] = dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }
    // <PEAK>
    if (qName.equals(PeakListElementName_2_0.PEAK.getElementName())) {
        DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
        Range<Double> 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 = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            if (mz > 0.0) {
                mzPeaks[i] = new SimpleDataPoint(mz, intensity);
                if (peakMZRange == null)
                    peakMZRange = Range.singleton(mz);
                else
                    peakMZRange = peakMZRange.span(Range.singleton(mz));
            }
        }
        FeatureStatus status = FeatureStatus.valueOf(peakStatus);
        // convert vector of allMS2FragmentScans to array
        allMS2FragmentScanNumbers = new int[currentAllMS2FragmentScans.size()];
        for (int i = 0; i < allMS2FragmentScanNumbers.length; i++) {
            allMS2FragmentScanNumbers[i] = currentAllMS2FragmentScans.get(i);
        }
        // clear all MS2 fragment scan numbers list for next peak
        currentAllMS2FragmentScans.clear();
        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status, representativeScan, fragmentScan, allMS2FragmentScanNumbers, 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_0.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }
    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_0.PEAK_IDENTITY.getElementName())) {
        String content = getTextOfElement();
        if (identityProperties.get(PeakIdentity.PROPERTY_NAME) == null)
            identityProperties.put(PeakIdentity.PROPERTY_NAME, content);
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }
    // <ROW>
    if (qName.equals(PeakListElementName_2_0.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }
    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_0.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_0.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }
    if (qName.equals(PeakListElementName_2_0.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }
}

Example 27 with SimpleFeature

use of net.sf.mzmine.datamodel.impl.SimpleFeature in project mzmine2 by mzmine.

the class PeakListOpenHandler_2_3 method endElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
 *      java.lang.String)
 */
@Override
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 feature 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 feature 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());
    }
    if (qName.equals(PeakListElementName_2_3.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }
    // <All_MS2_FRAGMENT_SCANS>
    if (qName.equals(PeakListElementName_2_5.ALL_MS2_FRAGMENT_SCANS.getElementName())) {
        Integer fragmentNumber = Integer.valueOf(getTextOfElement());
        currentAllMS2FragmentScans.add(fragmentNumber);
    }
    // <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] = 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] = dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }
    // <PEAK>
    if (qName.equals(PeakListElementName_2_3.PEAK.getElementName())) {
        DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
        Range<Double> 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 = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            if (mz > 0.0) {
                mzPeaks[i] = new SimpleDataPoint(mz, intensity);
                if (peakMZRange == null)
                    peakMZRange = Range.singleton(mz);
                else
                    peakMZRange = peakMZRange.span(Range.singleton(mz));
            }
        }
        FeatureStatus status = FeatureStatus.valueOf(peakStatus);
        // convert vector of allMS2FragmentScans to array
        allMS2FragmentScanNumbers = new int[currentAllMS2FragmentScans.size()];
        for (int i = 0; i < allMS2FragmentScanNumbers.length; i++) {
            allMS2FragmentScanNumbers[i] = currentAllMS2FragmentScans.get(i);
        }
        // clear all MS2 fragment scan numbers list for next peak
        currentAllMS2FragmentScans.clear();
        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status, representativeScan, fragmentScan, allMS2FragmentScanNumbers, 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);
    }
}

Example 28 with SimpleFeature

use of net.sf.mzmine.datamodel.impl.SimpleFeature in project mzmine2 by mzmine.

the class MsMsPeakPickingTask method run.

@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    final Scan[] scans = scanSelection.getMatchingScans(dataFile);
    totalScans = scans.length;
    for (Scan scan : scans) {
        if (isCanceled())
            return;
        // Get the MS Scan
        Scan bestScan = null;
        Range<Double> rtWindow = Range.closed(scan.getRetentionTime() - (binTime / 2.0), scan.getRetentionTime() + (binTime / 2.0));
        Range<Double> mzWindow = Range.closed(scan.getPrecursorMZ() - (binSize / 2.0), scan.getPrecursorMZ() + (binSize / 2.0));
        DataPoint point;
        DataPoint maxPoint = null;
        int[] regionScanNumbers = dataFile.getScanNumbers(1, rtWindow);
        for (int regionScanNumber : regionScanNumbers) {
            Scan regionScan = dataFile.getScan(regionScanNumber);
            point = ScanUtils.findBasePeak(regionScan, mzWindow);
            // no datapoint found
            if (point == null) {
                continue;
            }
            if (maxPoint == null) {
                maxPoint = point;
            }
            int result = Double.compare(maxPoint.getIntensity(), point.getIntensity());
            if (result <= 0) {
                maxPoint = point;
                bestScan = regionScan;
            }
        }
        // if no representative dataPoint
        if (bestScan == null) {
            continue;
        }
        assert maxPoint != null;
        SimpleFeature c = new SimpleFeature(dataFile, scan.getPrecursorMZ(), bestScan.getRetentionTime(), maxPoint.getIntensity(), maxPoint.getIntensity(), new int[] { bestScan.getScanNumber() }, new DataPoint[] { maxPoint }, FeatureStatus.DETECTED, bestScan.getScanNumber(), scan.getScanNumber(), new int[] {}, Range.singleton(bestScan.getRetentionTime()), Range.singleton(scan.getPrecursorMZ()), Range.singleton(maxPoint.getIntensity()));
        PeakListRow entry = new SimplePeakListRow(scan.getScanNumber());
        entry.addPeak(dataFile, c);
        newPeakList.addRow(entry);
        processedScans++;
    }
    project.addPeakList(newPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(newPeakList);
    logger.info("Finished MS/MS peak builder on " + dataFile + ", " + processedScans + " scans processed");
    setStatus(TaskStatus.FINISHED);
}