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

Example 6 with SimplePeakList

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

the class RansacAlignerTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running Ransac aligner");
    // twice, first for score calculation, second for actual alignment.
    for (int i = 0; i < peakLists.length; i++) {
        totalRows += peakLists[i].getNumberOfRows() * 2;
    }
    // Collect all data files
    List<RawDataFile> allDataFiles = new ArrayList<RawDataFile>();
    for (PeakList peakList : peakLists) {
        for (RawDataFile dataFile : peakList.getRawDataFiles()) {
            // Each data file can only have one column in aligned feature list
            if (allDataFiles.contains(dataFile)) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage("Cannot run alignment, because file " + dataFile + " is present in multiple feature lists");
                return;
            }
            allDataFiles.add(dataFile);
        }
    }
    // Create a new aligned feature list
    alignedPeakList = new SimplePeakList(peakListName, allDataFiles.toArray(new RawDataFile[0]));
    // Iterate source feature lists
    for (PeakList peakList : peakLists) {
        HashMap<PeakListRow, PeakListRow> alignmentMapping = this.getAlignmentMap(peakList);
        PeakListRow[] allRows = peakList.getRows();
        // Align all rows using mapping
        for (PeakListRow row : allRows) {
            PeakListRow targetRow = alignmentMapping.get(row);
            // If we have no mapping for this row, add a new one
            if (targetRow == null) {
                targetRow = new SimplePeakListRow(newRowID);
                newRowID++;
                alignedPeakList.addRow(targetRow);
            }
            // Add all peaks from the original row to the aligned row
            for (RawDataFile file : row.getRawDataFiles()) {
                targetRow.addPeak(file, row.getPeak(file));
            }
            // Add all non-existing identities from the original row to the
            // aligned row
            PeakUtils.copyPeakListRowProperties(row, targetRow);
            processedRows++;
        }
    }
    // Next feature list
    // Add new aligned feature list to the project
    project.addPeakList(alignedPeakList);
    // Edit by Aleksandr Smirnov
    PeakListRow row = alignedPeakList.getRow(1);
    double alignedRetTime = row.getAverageRT();
    for (Feature peak : row.getPeaks()) {
        double retTimeDelta = alignedRetTime - peak.getRT();
        RawDataFile dataFile = peak.getDataFile();
        SortedMap<Double, Double> chromatogram = new TreeMap<>();
        for (int scan : peak.getScanNumbers()) {
            DataPoint dataPoint = peak.getDataPoint(scan);
            double retTime = dataFile.getScan(scan).getRetentionTime() + retTimeDelta;
            if (dataPoint != null)
                chromatogram.put(retTime, dataPoint.getIntensity());
        }
    }
    // End of Edit
    // Add task description to peakList
    alignedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Ransac aligner", parameters));
    logger.info("Finished RANSAC aligner");
    setStatus(TaskStatus.FINISHED);
}

Example 7 with SimplePeakList

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

the class MultiRawDataLearnerTask method run.

/**
 * @see Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running learner task on " + peakList);
    // Create a new results peakList which is added at the end
    resultPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    /**
     * - A PeakList is a list of Features (peak in retention time dimension with accurate m/z)<br>
     * ---- contains one or multiple RawDataFiles <br>
     * ---- access mean retention time, mean m/z, maximum intensity, ...<br>
     * - A RawDataFile holds a full chromatographic run with all ms scans<br>
     * ---- Each Scan and the underlying raw data can be accessed <br>
     * ---- Scans can be filtered by MS level, polarity, ...<br>
     */
    // get all rows and sort by m/z
    PeakListRow[] rows = peakList.getRows();
    Arrays.sort(rows, new PeakListRowSorter(SortingProperty.MZ, SortingDirection.Ascending));
    // number of rawFiles is 1 prior to peaklist alignment
    RawDataFile[] rawFiles = peakList.getRawDataFiles();
    boolean isAlignedPeakList = rawFiles.length > 1;
    totalRows = rows.length;
    // loop through all rows
    for (PeakListRow row : rows) {
        // loop through all raw data files
        for (RawDataFile raw : rawFiles) {
            // check for cancelled state and stop
            if (isCanceled())
                return;
            // current peak
            Feature peak = row.getPeak(raw);
            // check for peak in row for specific raw file
            if (peak != null) {
                double mz = peak.getMZ();
                double intensity = peak.getHeight();
                double rt = peak.getRT();
            // do stuff
            // ...
            }
        }
        // Update completion rate
        processedRows++;
    }
    // add to project
    addResultToProject();
    logger.info("Finished on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 8 with SimplePeakList

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

the class PeakLearnerTask method run.

/**
 * @see Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running learner task on " + peakList);
    // Create a new results peakList which is added at the end
    resultPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    /**
     * - A PeakList is a list of Features (peak in retention time dimension with accurate m/z)<br>
     * ---- contains one or multiple RawDataFiles <br>
     * ---- access mean retention time, mean m/z, maximum intensity, ...<br>
     * - A RawDataFile holds a full chromatographic run with all ms scans<br>
     * ---- Each Scan and the underlying raw data can be accessed <br>
     * ---- Scans can be filtered by MS level, polarity, ...<br>
     */
    // is the data provided by peaklist enough for this task or
    // do you want to work on one raw data file or on all files?
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // get all peaks of a raw data file
    // Sort peaks by ascending mz
    Feature[] sortedPeaks = peakList.getPeaks(dataFile);
    Arrays.sort(sortedPeaks, new PeakSorter(SortingProperty.MZ, SortingDirection.Ascending));
    // Loop through all peaks
    totalPeaks = sortedPeaks.length;
    for (int i = 0; i < totalPeaks; i++) {
        // check for cancelled state and stop
        if (isCanceled())
            return;
        // current peak
        Feature aPeak = sortedPeaks[i];
        // do stuff
        // ...
        // add row to result feature list
        PeakListRow row = peakList.getPeakRow(aPeak);
        row = copyPeakRow(row);
        resultPeakList.addRow(row);
        // Update completion rate
        processedPeaks++;
    }
    // add to project
    addResultToProject();
    logger.info("Finished on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 9 with SimplePeakList

use of net.sf.mzmine.datamodel.impl.SimplePeakList 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 10 with SimplePeakList

use of net.sf.mzmine.datamodel.impl.SimplePeakList 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);
}