Examples with PeakListAppliedMethod net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod used on opensource projects

Example 1 with PeakListAppliedMethod

use of net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod in project mzmine2 by mzmine.

the class IsotopeGrouperTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running isotopic peak grouper on " + peakList);
    // We assume source peakList contains one datafile
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create a new deisotoped peakList
    deisotopedPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    // Collect all selected charge states
    int[] charges = new int[maximumCharge];
    for (int i = 0; i < maximumCharge; i++) charges[i] = i + 1;
    // 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;
    for (int ind = 0; ind < totalPeaks; ind++) {
        if (isCanceled())
            return;
        Feature aPeak = sortedPeaks[ind];
        // Check if peak was already deleted
        if (aPeak == null) {
            processedPeaks++;
            continue;
        }
        // Check which charge state fits best around this peak
        int bestFitCharge = 0;
        int bestFitScore = -1;
        Vector<Feature> bestFitPeaks = null;
        for (int charge : charges) {
            Vector<Feature> fittedPeaks = new Vector<Feature>();
            fittedPeaks.add(aPeak);
            fitPattern(fittedPeaks, aPeak, charge, sortedPeaks);
            int score = fittedPeaks.size();
            if ((score > bestFitScore) || ((score == bestFitScore) && (bestFitCharge > charge))) {
                bestFitScore = score;
                bestFitCharge = charge;
                bestFitPeaks = fittedPeaks;
            }
        }
        PeakListRow oldRow = peakList.getPeakRow(aPeak);
        assert bestFitPeaks != null;
        // isotope, we skip this left the original peak in the feature list.
        if (bestFitPeaks.size() == 1) {
            deisotopedPeakList.addRow(oldRow);
            processedPeaks++;
            continue;
        }
        // Convert the peak pattern to array
        Feature[] originalPeaks = bestFitPeaks.toArray(new Feature[0]);
        // Create a new SimpleIsotopePattern
        DataPoint[] isotopes = new DataPoint[bestFitPeaks.size()];
        for (int i = 0; i < isotopes.length; i++) {
            Feature p = originalPeaks[i];
            isotopes[i] = new SimpleDataPoint(p.getMZ(), p.getHeight());
        }
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(isotopes, IsotopePatternStatus.DETECTED, aPeak.toString());
        // the lowest m/z peak
        if (chooseMostIntense) {
            Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
        } else {
            Arrays.sort(originalPeaks, new PeakSorter(SortingProperty.MZ, SortingDirection.Ascending));
        }
        Feature newPeak = new SimpleFeature(originalPeaks[0]);
        newPeak.setIsotopePattern(newPattern);
        newPeak.setCharge(bestFitCharge);
        // Keep old ID
        int oldID = oldRow.getID();
        SimplePeakListRow newRow = new SimplePeakListRow(oldID);
        PeakUtils.copyPeakListRowProperties(oldRow, newRow);
        newRow.addPeak(dataFile, newPeak);
        deisotopedPeakList.addRow(newRow);
        // Remove all peaks already assigned to isotope pattern
        for (int i = 0; i < sortedPeaks.length; i++) {
            if (bestFitPeaks.contains(sortedPeaks[i]))
                sortedPeaks[i] = null;
        }
        // Update completion rate
        processedPeaks++;
    }
    // Add new peakList to the project
    project.addPeakList(deisotopedPeakList);
    // Load previous applied methods
    for (PeakListAppliedMethod proc : peakList.getAppliedMethods()) {
        deisotopedPeakList.addDescriptionOfAppliedTask(proc);
    }
    // Add task description to peakList
    deisotopedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Isotopic peaks grouper", parameters));
    // Remove the original peakList if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    logger.info("Finished isotopic peak grouper on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 2 with PeakListAppliedMethod

use of net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod in project mzmine2 by mzmine.

the class PeakListOpenHandler_2_5 method initializePeakList.

/**
 * Initializes the feature list
 */
private void initializePeakList() {
    RawDataFile[] dataFiles = currentPeakListDataFiles.toArray(new RawDataFile[0]);
    buildingPeakList = new SimplePeakList(peakListName, dataFiles);
    for (int i = 0; i < appliedMethods.size(); i++) {
        String methodName = appliedMethods.elementAt(i);
        String methodParams = appliedMethodParameters.elementAt(i);
        PeakListAppliedMethod pam = new SimplePeakListAppliedMethod(methodName, methodParams);
        buildingPeakList.addDescriptionOfAppliedTask(pam);
    }
    buildingPeakList.setDateCreated(dateCreated);
}

Example 3 with PeakListAppliedMethod

use of net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod 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 4 with PeakListAppliedMethod

use of net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod in project mzmine2 by mzmine.

the class PeakListOpenHandler_2_0 method initializePeakList.

/**
 * Initializes the feature list
 */
private void initializePeakList() {
    RawDataFile[] dataFiles = currentPeakListDataFiles.toArray(new RawDataFile[0]);
    buildingPeakList = new SimplePeakList(peakListName, dataFiles);
    for (int i = 0; i < appliedMethods.size(); i++) {
        String methodName = appliedMethods.elementAt(i);
        String methodParams = appliedMethodParameters.elementAt(i);
        PeakListAppliedMethod pam = new SimplePeakListAppliedMethod(methodName, methodParams);
        buildingPeakList.addDescriptionOfAppliedTask(pam);
    }
    buildingPeakList.setDateCreated(dateCreated);
}

Example 5 with PeakListAppliedMethod

use of net.sf.mzmine.datamodel.PeakList.PeakListAppliedMethod in project mzmine2 by mzmine.

the class PeakListOpenHandler_2_3 method initializePeakList.

/**
 * Initializes the feature list
 */
private void initializePeakList() {
    RawDataFile[] dataFiles = currentPeakListDataFiles.toArray(new RawDataFile[0]);
    buildingPeakList = new SimplePeakList(peakListName, dataFiles);
    for (int i = 0; i < appliedMethods.size(); i++) {
        String methodName = appliedMethods.elementAt(i);
        String methodParams = appliedMethodParameters.elementAt(i);
        PeakListAppliedMethod pam = new SimplePeakListAppliedMethod(methodName, methodParams);
        buildingPeakList.addDescriptionOfAppliedTask(pam);
    }
    buildingPeakList.setDateCreated(dateCreated);
}