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

Example 6 with PeakIdentity

use of net.sf.mzmine.datamodel.PeakIdentity 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 7 with PeakIdentity

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

the class ScatterPlotItemLabelGenerator method generateLabel.

/**
 * @see org.jfree.chart.labels.XYItemLabelGenerator#generateLabel(org.jfree.data.xy.XYDataset,
 *      int, int)
 */
public String generateLabel(XYDataset dataSet, int series, int item) {
    ScatterPlotDataSet scatterDataSet = (ScatterPlotDataSet) dataSet;
    PeakListRow row = scatterDataSet.getRow(series, item);
    PeakIdentity identity = row.getPreferredPeakIdentity();
    if (identity != null) {
        return identity.getName();
    } else {
        return row.toString();
    }
}

Example 8 with PeakIdentity

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

the class SearchDefinition method conforms.

/**
 * Checks whether given feature list row conforms to this search condition.
 */
public boolean conforms(PeakListRow row) {
    switch(type) {
        case NAME:
            PeakIdentity identity = row.getPreferredPeakIdentity();
            if (identity == null)
                return false;
            String name = identity.getName();
            if (isEmpty(nameRegex.toString()) || isEmpty(name)) {
                return false;
            }
            Matcher matcher = nameRegex.matcher(name);
            return matcher.find();
        case MASS:
            return range.contains(row.getAverageMZ());
        case RT:
            return range.contains(row.getAverageRT());
    }
    return false;
}

Example 9 with PeakIdentity

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

the class SameRangeTask method run.

public void run() {
    logger.info("Started gap-filling " + peakList);
    setStatus(TaskStatus.PROCESSING);
    // Get total number of rows
    totalRows = peakList.getNumberOfRows();
    // Get feature list columns
    RawDataFile[] columns = peakList.getRawDataFiles();
    // Create new feature list
    processedPeakList = new SimplePeakList(peakList + " " + suffix, columns);
    /**
     ***********************************************************
     * Creating a stream to process the data in parallel
     */
    processedRowsAtomic = new AtomicInteger(0);
    List<PeakListRow> outputList = Collections.synchronizedList(new ArrayList<>());
    peakList.parallelStream().forEach(sourceRow -> {
        // Canceled?
        if (isCanceled())
            return;
        PeakListRow newRow = new SimplePeakListRow(sourceRow.getID());
        // Copy comment
        newRow.setComment(sourceRow.getComment());
        // Copy identities
        for (PeakIdentity ident : sourceRow.getPeakIdentities()) newRow.addPeakIdentity(ident, false);
        if (sourceRow.getPreferredPeakIdentity() != null)
            newRow.setPreferredPeakIdentity(sourceRow.getPreferredPeakIdentity());
        // Copy each peaks and fill gaps
        for (RawDataFile column : columns) {
            // Canceled?
            if (isCanceled())
                return;
            // Get current peak
            Feature currentPeak = sourceRow.getPeak(column);
            // If there is a gap, try to fill it
            if (currentPeak == null)
                currentPeak = fillGap(sourceRow, column);
            // If a peak was found or created, add it
            if (currentPeak != null)
                newRow.addPeak(column, currentPeak);
        }
        outputList.add(newRow);
        processedRowsAtomic.getAndAdd(1);
    });
    outputList.stream().forEach(newRow -> {
        processedPeakList.addRow((PeakListRow) newRow);
    });
    // Canceled?
    if (isCanceled())
        return;
    // Append processed feature list to the project
    project.addPeakList(processedPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(processedPeakList);
    // Add task description to peakList
    processedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Gap filling using RT and m/z range", parameters));
    // Remove the original peaklist if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished gap-filling " + peakList);
}

Example 10 with PeakIdentity

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

the class CameraSearchTask method addPseudoSpectraIdentities.

/**
 * Add pseudo-spectra identities.
 *
 * @param peaks peaks to annotate with identities.
 * @param spectraExp the pseudo-spectra ids vector.
 * @param isotopeExp the isotopes vector.
 */
private void addPseudoSpectraIdentities(final Feature[] peaks, final int[] spectra, final String[] isotopes, final String[] adducts) {
    // Add identities for each peak.
    int peakIndex = 0;
    for (final Feature peak : peaks) {
        // Create pseudo-spectrum identity
        final SimplePeakIdentity identity = new SimplePeakIdentity("Pseudo-spectrum #" + String.format("%03d", spectra[peakIndex]));
        identity.setPropertyValue(PeakIdentity.PROPERTY_METHOD, "Bioconductor CAMERA");
        // Add isotope info, if any.
        if (isotopes != null) {
            final String isotope = isotopes[peakIndex].trim();
            if (isotope.length() > 0) {
                // Parse the isotope pattern.
                final Matcher matcher = ISOTOPE_PATTERN.matcher(isotope);
                if (matcher.matches()) {
                    // identity.setPropertyValue("Isotope", matcher.group(1));
                    identity.setPropertyValue("Isotope", isotope);
                } else {
                    LOG.warning("Irregular isotope value: " + isotope);
                }
            }
        }
        if (adducts != null) {
            final String adduct = adducts[peakIndex].trim();
            if (adduct.length() > 0)
                identity.setPropertyValue("Adduct", adduct);
        }
        // Add identity to peak's row.
        PeakListRow row = peakList.getPeakRow(peak);
        for (PeakIdentity peakIdentity : row.getPeakIdentities()) row.removePeakIdentity(peakIdentity);
        peakList.getPeakRow(peak).addPeakIdentity(identity, true);
        peakIndex++;
    }
}