Examples with Feature net.sf.mzmine.datamodel.Feature used on opensource projects

Example 31 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class PeakListSaveHandler method fillRowElement.

/**
 * Add the row information into the XML document
 *
 * @param row
 * @param element
 * @throws IOException
 */
private void fillRowElement(PeakListRow row, TransformerHandler hd) throws SAXException, IOException {
    // <PEAK_IDENTITY>
    PeakIdentity preferredIdentity = row.getPreferredPeakIdentity();
    PeakIdentity[] identities = row.getPeakIdentities();
    AttributesImpl atts = new AttributesImpl();
    for (int i = 0; i < identities.length; i++) {
        if (canceled)
            return;
        atts.addAttribute("", "", PeakListElementName.ID.getElementName(), "CDATA", String.valueOf(i));
        atts.addAttribute("", "", PeakListElementName.PREFERRED.getElementName(), "CDATA", String.valueOf(identities[i] == preferredIdentity));
        hd.startElement("", "", PeakListElementName.PEAK_IDENTITY.getElementName(), atts);
        fillIdentityElement(identities[i], hd);
        hd.endElement("", "", PeakListElementName.PEAK_IDENTITY.getElementName());
    }
    if (canceled)
        return;
    // atts.addAttribute("", "", PeakListElementName.ID.getElementName(),
    // "CDATA", "INFORMATION");
    hd.startElement("", "", PeakListElementName.PEAK_INFORMATION.getElementName(), atts);
    fillInformationElement(row.getPeakInformation(), hd);
    hd.endElement("", "", PeakListElementName.PEAK_INFORMATION.getElementName());
    // <PEAK>
    Feature[] peaks = row.getPeaks();
    for (Feature p : peaks) {
        if (canceled)
            return;
        atts.clear();
        String dataFileID = dataFilesIDMap.get(p.getDataFile());
        atts.addAttribute("", "", PeakListElementName.COLUMN.getElementName(), "CDATA", dataFileID);
        atts.addAttribute("", "", PeakListElementName.MZ.getElementName(), "CDATA", String.valueOf(p.getMZ()));
        // In the project file, retention time is represented in seconds,
        // for historical reasons
        double rt = p.getRT() * 60d;
        atts.addAttribute("", "", PeakListElementName.RT.getElementName(), "CDATA", String.valueOf(rt));
        atts.addAttribute("", "", PeakListElementName.HEIGHT.getElementName(), "CDATA", String.valueOf(p.getHeight()));
        atts.addAttribute("", "", PeakListElementName.AREA.getElementName(), "CDATA", String.valueOf(p.getArea()));
        atts.addAttribute("", "", PeakListElementName.STATUS.getElementName(), "CDATA", p.getFeatureStatus().toString());
        atts.addAttribute("", "", PeakListElementName.CHARGE.getElementName(), "CDATA", String.valueOf(p.getCharge()));
        atts.addAttribute("", "", PeakListElementName.PARENT_CHROMATOGRAM_ROW_ID.getElementName(), "CDATA", p.getParentChromatogramRowID() != null ? String.valueOf(p.getParentChromatogramRowID()) : "");
        hd.startElement("", "", PeakListElementName.PEAK.getElementName(), atts);
        fillPeakElement(p, hd);
        hd.endElement("", "", PeakListElementName.PEAK.getElementName());
    }
}

Example 32 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class ChromatogramBuilderTask method run.

/**
 * @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 feature 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 feature 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);
}

Example 33 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class ShapeModelerTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    Class<?> shapeModelClass = shapeModelerType.getModelClass();
    Constructor<?> shapeModelConstruct;
    shapeModelConstruct = shapeModelClass.getConstructors()[0];
    // Get data file information
    RawDataFile dataFile = originalPeakList.getRawDataFile(0);
    // Create new feature list
    newPeakList = new SimplePeakList(originalPeakList + " " + suffix, dataFile);
    totalRows = originalPeakList.getNumberOfRows();
    int[] scanNumbers;
    double[] retentionTimes, intensities;
    SimplePeakListRow newRow;
    for (PeakListRow row : originalPeakList.getRows()) {
        if (isCanceled())
            return;
        newRow = new SimplePeakListRow(newPeakID);
        try {
            for (Feature peak : row.getPeaks()) {
                // Load the intensities into array
                dataFile = peak.getDataFile();
                scanNumbers = peak.getScanNumbers();
                retentionTimes = new double[scanNumbers.length];
                for (int i = 0; i < scanNumbers.length; i++) retentionTimes[i] = dataFile.getScan(scanNumbers[i]).getRetentionTime();
                intensities = new double[scanNumbers.length];
                for (int i = 0; i < scanNumbers.length; i++) {
                    DataPoint dp = peak.getDataPoint(scanNumbers[i]);
                    if (dp != null)
                        intensities[i] = dp.getIntensity();
                    else
                        intensities[i] = 0;
                }
                Feature shapePeak = (Feature) shapeModelConstruct.newInstance(peak, scanNumbers, intensities, retentionTimes, resolution);
                newRow.addPeak(shapePeak.getDataFile(), shapePeak);
            }
        } catch (Exception e) {
            String message = "Error trying to make an instance of shape model class " + shapeModelClass;
            MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), message);
            logger.severe(message);
            return;
        }
        newPeakList.addRow(newRow);
        newPeakID++;
        processedRows++;
    }
    // Add new peaklist to the project
    project.addPeakList(newPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(newPeakList);
    // Remove the original peaklist if requested
    if (removeOriginal)
        project.removePeakList(originalPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : originalPeakList.getAppliedMethods()) {
        newPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    newPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peaks shaped by " + shapeModelerType + " function", parameters));
    logger.finest("Finished peak shape modeler " + processedRows + " rows processed");
    setStatus(TaskStatus.FINISHED);
}

Example 34 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class PeakExtenderTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running peak extender on " + peakList);
    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create a new deisotoped peakList
    extendedPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    // Sort peaks by descending height
    Feature[] sortedPeaks = peakList.getPeaks(dataFile);
    Arrays.sort(sortedPeaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
    // Loop through all peaks
    totalPeaks = sortedPeaks.length;
    Feature oldPeak;
    for (int ind = 0; ind < totalPeaks; ind++) {
        if (isCanceled())
            return;
        oldPeak = sortedPeaks[ind];
        if (oldPeak.getHeight() >= minimumHeight) {
            Feature newPeak = this.getExtendedPeak(oldPeak);
            // Get previous pekaListRow
            PeakListRow oldRow = peakList.getPeakRow(oldPeak);
            // keep old ID
            int oldID = oldRow.getID();
            SimplePeakListRow newRow = new SimplePeakListRow(oldID);
            PeakUtils.copyPeakListRowProperties(oldRow, newRow);
            newRow.addPeak(dataFile, newPeak);
            extendedPeakList.addRow(newRow);
        }
        // Update completion rate
        processedPeaks++;
    }
    // Add new peakList to the project
    project.addPeakList(extendedPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(extendedPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : peakList.getAppliedMethods()) {
        extendedPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    extendedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peak extender", parameters));
    // Remove the original peakList if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    logger.info("Finished peak extender on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 35 with Feature

use of net.sf.mzmine.datamodel.Feature in project mzmine2 by mzmine.

the class ShapeModelerSetupDialog method loadPreviewPeak.

private void loadPreviewPeak() {
    PeakListRow previewRow = (PeakListRow) comboPeak.getSelectedItem();
    if (previewRow == null)
        return;
    logger.finest("Loading new preview peak " + previewRow);
    Feature previewPeak = previewRow.getPeaks()[0];
    ticPlot.removeAllTICDataSets();
    // Load the intensities into array
    RawDataFile dataFile = previewPeak.getDataFile();
    int[] scanNumbers = previewPeak.getScanNumbers();
    double[] retentionTimes = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++) retentionTimes[i] = dataFile.getScan(scanNumbers[i]).getRetentionTime();
    double[] intensities = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++) {
        DataPoint dp = previewPeak.getDataPoint(scanNumbers[i]);
        if (dp != null)
            intensities[i] = dp.getIntensity();
        else
            intensities[i] = 0;
    }
    // Create shape model
    updateParameterSetFromComponents();
    JComboBox<?> component = (JComboBox<?>) getComponentForParameter(ShapeModelerParameters.shapeModelerType);
    ShapeModel model = (ShapeModel) component.getSelectedItem();
    JFormattedTextField resolutionField = (JFormattedTextField) getComponentForParameter(ShapeModelerParameters.massResolution);
    double resolution = ((Number) resolutionField.getValue()).doubleValue();
    try {
        Class<?> shapeModelClass = model.getModelClass();
        Constructor<?> shapeModelConstruct = shapeModelClass.getConstructors()[0];
        // shapePeakModel(ChromatographicPeak originalDetectedShape, int[]
        // scanNumbers,
        // double[] intensities, double[] retentionTimes, double resolution)
        Feature shapePeak = (Feature) shapeModelConstruct.newInstance(previewPeak, scanNumbers, intensities, retentionTimes, resolution);
        PeakDataSet peakDataSet = new PeakDataSet(shapePeak);
        ticPlot.addPeakDataset(peakDataSet);
        ticDataset = new ChromatogramTICDataSet(previewRow.getPeaks()[0]);
        ticPlot.addTICDataset(ticDataset);
        // Set auto range to axes
        ticPlot.getXYPlot().getDomainAxis().setAutoRange(true);
        ticPlot.getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
        ticPlot.getXYPlot().getRangeAxis().setAutoRange(true);
        ticPlot.getXYPlot().getRangeAxis().setAutoTickUnitSelection(true);
    } catch (Exception e) {
        String message = "Error trying to make an instance of Peak Builder " + model;
        MZmineCore.getDesktop().displayErrorMessage(this, message);
        logger.severe(message);
        e.printStackTrace();
        return;
    }
}