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

Example 21 with PeakListRow

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

the class ManualPickerTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.finest("Starting manual peak picker, RT: " + rtRange + ", m/z: " + mzRange);
    // Calculate total number of scans to process
    for (RawDataFile dataFile : dataFiles) {
        int[] scanNumbers = dataFile.getScanNumbers(1, rtRange);
        totalScans += scanNumbers.length;
    }
    // Find peak in each data file
    for (RawDataFile dataFile : dataFiles) {
        ManualPeak newPeak = new ManualPeak(dataFile);
        boolean dataPointFound = false;
        int[] scanNumbers = dataFile.getScanNumbers(1, rtRange);
        for (int scanNumber : scanNumbers) {
            if (isCanceled())
                return;
            // Get next scan
            Scan scan = dataFile.getScan(scanNumber);
            // Find most intense m/z peak
            DataPoint basePeak = ScanUtils.findBasePeak(scan, mzRange);
            if (basePeak != null) {
                if (basePeak.getIntensity() > 0)
                    dataPointFound = true;
                newPeak.addDatapoint(scan.getScanNumber(), basePeak);
            } else {
                final double mzCenter = (mzRange.lowerEndpoint() + mzRange.upperEndpoint()) / 2.0;
                DataPoint fakeDataPoint = new SimpleDataPoint(mzCenter, 0);
                newPeak.addDatapoint(scan.getScanNumber(), fakeDataPoint);
            }
            processedScans++;
        }
        if (dataPointFound) {
            newPeak.finalizePeak();
            if (newPeak.getArea() > 0)
                peakListRow.addPeak(dataFile, newPeak);
        } else {
            peakListRow.removePeak(dataFile);
        }
    }
    // Notify the GUI that peaklist contents have changed
    if (peakList != null) {
        // Check if the feature list row has been added to the feature list, and
        // if it has not, add it
        List<PeakListRow> rows = Arrays.asList(peakList.getRows());
        if (!rows.contains(peakListRow)) {
            peakList.addRow(peakListRow);
        }
        // Add quality parameters to peaks
        QualityParameters.calculateQualityParameters(peakList);
        project.notifyObjectChanged(peakList, true);
    }
    if (table != null) {
        ((AbstractTableModel) table.getModel()).fireTableDataChanged();
    }
    logger.finest("Finished manual peak picker, " + processedScans + " scans processed");
    setStatus(TaskStatus.FINISHED);
}

Example 22 with PeakListRow

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

the class ADAP3AlignerTask method findPeakListRow.

/**
 * Find the existing {@link PeakListRow} for a given feature list ID and row ID.
 *
 * @param peakListID number of a feature list in the array of {@link PeakList}. The numeration starts with 0.
 * @param rowID integer that is returned by method getId() of {@link PeakListRow}.
 * @return an instance of {@link PeakListRow} if an existing row is found. Otherwise it returns null.
 */
@Nullable
private PeakListRow findPeakListRow(final int peakListID, final int rowID) {
    // Find feature list
    PeakList peakList = findPeakList(peakListID);
    if (peakList == null)
        return null;
    // Find row
    PeakListRow row = null;
    for (final PeakListRow r : peakList.getRows()) if (rowID == r.getID()) {
        row = r;
        break;
    }
    return row;
}

Example 23 with PeakListRow

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

the class PeakListSaveHandler method savePeakList.

/**
 * Create an XML document with the feature list information an save it into the project zip file
 *
 * @param peakList
 * @param peakListSavedName name of the feature list
 * @throws java.io.IOException
 */
public void savePeakList(PeakList peakList) throws IOException, TransformerConfigurationException, SAXException {
    numberOfRows = peakList.getNumberOfRows();
    finishedRows = 0;
    StreamResult streamResult = new StreamResult(finalStream);
    SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance();
    TransformerHandler hd = tf.newTransformerHandler();
    Transformer serializer = hd.getTransformer();
    serializer.setOutputProperty(OutputKeys.INDENT, "yes");
    serializer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
    hd.setResult(streamResult);
    hd.startDocument();
    AttributesImpl atts = new AttributesImpl();
    hd.startElement("", "", PeakListElementName.PEAKLIST.getElementName(), atts);
    atts.clear();
    // <NAME>
    hd.startElement("", "", PeakListElementName.PEAKLIST_NAME.getElementName(), atts);
    hd.characters(peakList.getName().toCharArray(), 0, peakList.getName().length());
    hd.endElement("", "", PeakListElementName.PEAKLIST_NAME.getElementName());
    // <PEAKLIST_DATE>
    String dateText = "";
    if (((SimplePeakList) peakList).getDateCreated() == null) {
        dateText = ((SimplePeakList) peakList).getDateCreated();
    } else {
        Date date = new Date();
        dateText = dateFormat.format(date);
    }
    hd.startElement("", "", PeakListElementName.PEAKLIST_DATE.getElementName(), atts);
    hd.characters(dateText.toCharArray(), 0, dateText.length());
    hd.endElement("", "", PeakListElementName.PEAKLIST_DATE.getElementName());
    // <QUANTITY>
    hd.startElement("", "", PeakListElementName.QUANTITY.getElementName(), atts);
    hd.characters(String.valueOf(numberOfRows).toCharArray(), 0, String.valueOf(numberOfRows).length());
    hd.endElement("", "", PeakListElementName.QUANTITY.getElementName());
    // <PROCESS>
    PeakListAppliedMethod[] processes = peakList.getAppliedMethods();
    for (PeakListAppliedMethod proc : processes) {
        hd.startElement("", "", PeakListElementName.METHOD.getElementName(), atts);
        hd.startElement("", "", PeakListElementName.METHOD_NAME.getElementName(), atts);
        String methodName = proc.getDescription();
        hd.characters(methodName.toCharArray(), 0, methodName.length());
        hd.endElement("", "", PeakListElementName.METHOD_NAME.getElementName());
        hd.startElement("", "", PeakListElementName.METHOD_PARAMETERS.getElementName(), atts);
        String methodParameters = proc.getParameters();
        hd.characters(methodParameters.toCharArray(), 0, methodParameters.length());
        hd.endElement("", "", PeakListElementName.METHOD_PARAMETERS.getElementName());
        hd.endElement("", "", PeakListElementName.METHOD.getElementName());
    }
    atts.clear();
    // <RAWFILE>
    RawDataFile[] dataFiles = peakList.getRawDataFiles();
    for (int i = 0; i < dataFiles.length; i++) {
        String ID = dataFilesIDMap.get(dataFiles[i]);
        hd.startElement("", "", PeakListElementName.RAWFILE.getElementName(), atts);
        char[] idChars = ID.toCharArray();
        hd.characters(idChars, 0, idChars.length);
        hd.endElement("", "", PeakListElementName.RAWFILE.getElementName());
    }
    // <ROW>
    PeakListRow row;
    for (int i = 0; i < numberOfRows; i++) {
        if (canceled)
            return;
        atts.clear();
        row = peakList.getRow(i);
        atts.addAttribute("", "", PeakListElementName.ID.getElementName(), "CDATA", String.valueOf(row.getID()));
        if (row.getComment() != null) {
            atts.addAttribute("", "", PeakListElementName.COMMENT.getElementName(), "CDATA", row.getComment());
        }
        hd.startElement("", "", PeakListElementName.ROW.getElementName(), atts);
        fillRowElement(row, hd);
        hd.endElement("", "", PeakListElementName.ROW.getElementName());
        finishedRows++;
    }
    hd.endElement("", "", PeakListElementName.PEAKLIST.getElementName());
    hd.endDocument();
}

Example 24 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow 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 25 with PeakListRow

use of net.sf.mzmine.datamodel.PeakListRow 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);
}