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

Example 16 with SimpleScan

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

the class MzMLReadTask method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started parsing file " + file);
    MzMLUnmarshaller unmarshaller = new MzMLUnmarshaller(file);
    totalScans = unmarshaller.getObjectCountForXpath("/run/spectrumList/spectrum");
    fillScanIdTable(unmarshaller.unmarshalCollectionFromXpath("/run/spectrumList/spectrum", Spectrum.class), totalScans);
    MzMLObjectIterator<Spectrum> spectrumIterator = unmarshaller.unmarshalCollectionFromXpath("/run/spectrumList/spectrum", Spectrum.class);
    try {
        while (spectrumIterator.hasNext()) {
            if (isCanceled())
                return;
            Spectrum spectrum = spectrumIterator.next();
            // Ignore scans that are not MS, e.g. UV
            if (!isMsSpectrum(spectrum)) {
                parsedScans++;
                continue;
            }
            String scanId = spectrum.getId();
            Integer scanNumber = scanIdTable.get(scanId);
            if (scanNumber == null)
                throw new IllegalStateException("Cannot determine scan number: " + scanId);
            // Extract scan data
            int msLevel = extractMSLevel(spectrum);
            double retentionTime = extractRetentionTime(spectrum);
            PolarityType polarity = extractPolarity(spectrum);
            int parentScan = extractParentScanNumber(spectrum);
            double precursorMz = extractPrecursorMz(spectrum);
            int precursorCharge = extractPrecursorCharge(spectrum);
            String scanDefinition = extractScanDefinition(spectrum);
            DataPoint[] dataPoints = extractDataPoints(spectrum);
            // Auto-detect whether this scan is centroided
            MassSpectrumType spectrumType = ScanUtils.detectSpectrumType(dataPoints);
            SimpleScan scan = new SimpleScan(null, scanNumber, msLevel, retentionTime, precursorMz, precursorCharge, null, dataPoints, spectrumType, polarity, scanDefinition, null);
            for (SimpleScan s : parentStack) {
                if (s.getScanNumber() == parentScan) {
                    s.addFragmentScan(scanNumber);
                }
            }
            /*
         * Verify the size of parentStack. The actual size of the window to cover possible
         * candidates is defined by limitSize.
         */
            if (parentStack.size() > PARENT_STACK_SIZE) {
                SimpleScan firstScan = parentStack.removeLast();
                newMZmineFile.addScan(firstScan);
            }
            parentStack.addFirst(scan);
            parsedScans++;
        }
        while (!parentStack.isEmpty()) {
            SimpleScan scan = parentStack.removeLast();
            newMZmineFile.addScan(scan);
        }
        finalRawDataFile = newMZmineFile.finishWriting();
        project.addFile(finalRawDataFile);
    } catch (Throwable e) {
        e.printStackTrace();
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Error parsing mzML: " + ExceptionUtils.exceptionToString(e));
        e.printStackTrace();
        return;
    }
    if (parsedScans == 0) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("No scans found");
        return;
    }
    logger.info("Finished parsing " + file + ", parsed " + parsedScans + " scans");
    setStatus(TaskStatus.FINISHED);
}

Example 17 with SimpleScan

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

the class AgilentCsvReadTask method run.

/**
 * Reads the file.
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    Scanner scanner;
    try {
        scanner = new Scanner(this.file);
        this.dataSource = this.getMetaData(scanner, "file name");
        String[] range = this.getMetaData(scanner, "mass range").split(",");
        newMZmineFile.setMZRange(1, Range.closed(Double.parseDouble(range[0]), Double.parseDouble(range[1])));
        range = this.getMetaData(scanner, "time range").split(",");
        newMZmineFile.setRTRange(1, Range.closed(Double.parseDouble(range[0]), Double.parseDouble(range[1])));
        totalScans = Integer.parseInt(this.getMetaData(scanner, "number of spectra"));
        // advance to the spectrum data...
        while (!scanner.nextLine().trim().equals("[spectra]")) {
        }
        scanner.useDelimiter(",");
        for (parsedScans = 0; parsedScans < totalScans; parsedScans++) {
            if (isCanceled()) {
                return;
            }
            // if the task is canceled.
            double retentionTime = scanner.nextDouble();
            // not sure about this value
            int msLevel = scanner.nextInt();
            scanner.next();
            scanner.next();
            int charge = (scanner.next().equals("+") ? 1 : -1);
            scanner.next();
            int spectrumSize = scanner.nextInt();
            DataPoint[] dataPoints = new DataPoint[spectrumSize];
            for (int j = 0; j < spectrumSize; j++) {
                dataPoints[j] = new SimpleDataPoint(scanner.nextDouble(), scanner.nextDouble());
            }
            newMZmineFile.addScan(new SimpleScan(null, parsedScans + 1, msLevel, retentionTime, 0.0, charge, null, dataPoints, ScanUtils.detectSpectrumType(dataPoints), PolarityType.UNKNOWN, "", null));
            scanner.nextLine();
        }
        finalRawDataFile = newMZmineFile.finishWriting();
        project.addFile(finalRawDataFile);
    } catch (Exception e) {
        setErrorMessage(e.getMessage());
        this.setStatus(TaskStatus.ERROR);
        return;
    }
    this.setStatus(TaskStatus.FINISHED);
}