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

Example 1 with MassList

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

the class SingleRowPredictionTask method checkConstraints.

private void checkConstraints(IMolecularFormula cdkFormula) {
    // Check elemental ratios
    if (checkRatios) {
        boolean check = ElementalHeuristicChecker.checkFormula(cdkFormula, ratiosParameters);
        if (!check)
            return;
    }
    Double rdbeValue = RDBERestrictionChecker.calculateRDBE(cdkFormula);
    // Check RDBE condition
    if (checkRDBE && (rdbeValue != null)) {
        boolean check = RDBERestrictionChecker.checkRDBE(rdbeValue, rdbeParameters);
        if (!check)
            return;
    }
    // Calculate isotope similarity score
    final IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
    final String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
    final String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
    final double isotopeNoiseLevel = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
    // Fixed min abundance
    final double minPredictedAbundance = 0.00001;
    final IsotopePattern predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, minPredictedAbundance, charge, ionType.getPolarity());
    Double isotopeScore = null;
    if ((checkIsotopes) && (detectedPattern != null)) {
        isotopeScore = IsotopePatternScoreCalculator.getSimilarityScore(detectedPattern, predictedIsotopePattern, isotopeParameters);
        final double minScore = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopePatternScoreThreshold).getValue();
        if (isotopeScore < minScore)
            return;
    }
    // MS/MS evaluation is slowest, so let's do it last
    Double msmsScore = null;
    Feature bestPeak = peakListRow.getBestPeak();
    RawDataFile dataFile = bestPeak.getDataFile();
    Map<DataPoint, String> msmsAnnotations = null;
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
    if ((checkMSMS) && (msmsScanNumber > 0)) {
        Scan msmsScan = dataFile.getScan(msmsScanNumber);
        String massListName = msmsParameters.getParameter(MSMSScoreParameters.massList).getValue();
        MassList ms2MassList = msmsScan.getMassList(massListName);
        if (ms2MassList == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("The MS/MS scan #" + msmsScanNumber + " in file " + dataFile.getName() + " does not have a mass list called '" + massListName + "'");
            return;
        }
        MSMSScore score = MSMSScoreCalculator.evaluateMSMS(cdkFormula, msmsScan, msmsParameters);
        double minMSMSScore = msmsParameters.getParameter(MSMSScoreParameters.msmsMinScore).getValue();
        if (score != null) {
            msmsScore = score.getScore();
            msmsAnnotations = score.getAnnotation();
            // Check the MS/MS condition
            if (msmsScore < minMSMSScore)
                return;
        }
    }
    // Create a new formula entry
    final ResultFormula resultEntry = new ResultFormula(cdkFormula, predictedIsotopePattern, rdbeValue, isotopeScore, msmsScore, msmsAnnotations);
    // Add the new formula entry
    resultWindow.addNewListItem(resultEntry);
    foundFormulas++;
}

Example 2 with MassList

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

the class Ms2SearchTask method simpleMS2similarity.

private Ms2SearchResult simpleMS2similarity(Scan scanMS2A, Scan scanMS2B, double intensityThreshold, MZTolerance mzRange, String massList) {
    double runningScoreTotal = 0.0;
    double mzRangePPM = mzRange.getPpmTolerance();
    List<DataPoint> matchedIons = new ArrayList<DataPoint>();
    if (scanMS2A == null || scanMS2B == null) {
        return null;
    }
    // Fetch centroided data
    MassList massListA = scanMS2A.getMassList(massListName);
    MassList massListB = scanMS2B.getMassList(massListName);
    if (massListA == null) {
        // Will this work properly? As this function isn't directly the task?
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Scan " + scanMS2A.getDataFile().getName() + " #" + scanMS2A.getScanNumber() + " does not have a mass list " + massListName);
        return null;
    }
    if (massListB == null) {
        // Will this work properly? As this function isn't directly the task?
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Scan " + scanMS2B.getDataFile().getName() + " #" + scanMS2B.getScanNumber() + " does not have a mass list " + massListName);
        return null;
    }
    DataPoint[] ionsA = null;
    DataPoint[] ionsB = null;
    ionsA = massListA.getDataPoints();
    ionsB = massListB.getDataPoints();
    if (ionsA == null || ionsB == null || ionsA.length == 0 || ionsB.length == 0) {
        // ionsB = scanMS2B.getDataPointsOverIntensity(intensityThreshold);
        return null;
    }
    // Compare every ion peak in MS2 scan A, to every ion peak in MS2 scan B.
    double ionsBMaxMZ = ionsB[ionsB.length - 1].getMZ();
    for (int i = 0; i < ionsA.length; i++) {
        double iMZ = ionsA[i].getMZ();
        double mzRangeAbsolute = iMZ * 1e-6 * mzRangePPM;
        if (iMZ - mzRangeAbsolute > ionsBMaxMZ)
            // Potential speedup heuristic. If any i is greater than the max of j, no more
            break;
        for (int j = 0; j < ionsB.length; j++) {
            double jMZ = ionsB[j].getMZ();
            if (iMZ < jMZ - mzRangeAbsolute)
                // Potential speedup heuristic. iMZ smaller than jMZ. Skip the rest of the j's as
                break;
            if (Math.abs(iMZ - jMZ) < mzRangeAbsolute) {
                runningScoreTotal += ionsA[i].getIntensity() * ionsB[j].getIntensity();
                matchedIons.add(ionsA[i]);
            }
        }
    }
    Ms2SearchResult result = new Ms2SearchResult(runningScoreTotal, "simple", matchedIons);
    return result;
}

Example 3 with MassList

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

the class MSMSExportModule method exportMSMS.

public static void exportMSMS(PeakListRow row) {
    ParameterSet parameters = MZmineCore.getConfiguration().getModuleParameters(MSMSExportModule.class);
    ExitCode exitCode = parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
    if (exitCode != ExitCode.OK)
        return;
    File outputFile = parameters.getParameter(MSMSExportParameters.outputFile).getValue();
    String massListName = parameters.getParameter(MSMSExportParameters.massList).getValue();
    if ((outputFile == null) || (massListName == null))
        return;
    // Best peak always exists, because feature list row has at least one peak
    Feature bestPeak = row.getBestPeak();
    // Get the MS/MS scan number
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
    if (msmsScanNumber < 1) {
        MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "There is no MS/MS scan for peak " + bestPeak);
        return;
    }
    // MS/MS scan must exist, because msmsScanNumber was > 0
    Scan msmsScan = bestPeak.getDataFile().getScan(msmsScanNumber);
    MassList massList = msmsScan.getMassList(massListName);
    if (massList == null) {
        MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "There is no mass list called " + massListName + " for MS/MS scan #" + msmsScanNumber + " (" + bestPeak.getDataFile() + ")");
        return;
    }
    DataPoint[] peaks = massList.getDataPoints();
    try {
        FileWriter fileWriter = new FileWriter(outputFile);
        BufferedWriter writer = new BufferedWriter(fileWriter);
        for (DataPoint peak : peaks) {
            writer.write(peak.getMZ() + " " + peak.getIntensity());
            writer.newLine();
        }
        writer.close();
    } catch (Exception e) {
        e.printStackTrace();
        MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Error writing to file " + outputFile + ": " + ExceptionUtils.exceptionToString(e));
    }
}

Example 4 with MassList

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

the class MZDistributionHistoTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Starting to build mz distribution histogram for " + dataFile);
    // all selected scans
    scans = scanSelection.getMatchingScans(dataFile);
    totalScans = scans.length;
    // histo data
    DoubleArrayList data = new DoubleArrayList();
    for (Scan scan : scans) {
        if (isCanceled())
            return;
        // retention time in range
        if (!useRTRange || rtRange.contains(scan.getRetentionTime())) {
            // go through all mass lists
            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();
            // insert all mz in order and count them
            Arrays.stream(mzValues).mapToDouble(dp -> dp.getMZ()).filter(mz -> mzRange.contains(mz)).forEach(mz -> data.add(mz));
            processedScans++;
        }
    }
    if (!data.isEmpty()) {
        // to array
        double[] histo = new double[data.size()];
        for (int i = 0; i < data.size(); i++) histo[i] = data.get(i);
        // create histogram dialog
        EHistogramDialog dialog = new EHistogramDialog("m/z distribution", "m/z", new HistogramData(histo), binWidth);
        dialog.setVisible(true);
    } else {
        throw new MSDKRuntimeException("Data was empty. Review your selected filters.");
    }
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished mz distribution histogram on " + dataFile);
}

Example 5 with MassList

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

the class ProjectTreeMouseHandler method handleDoubleClickEvent.

private void handleDoubleClickEvent(MouseEvent e) {
    TreePath clickedPath = tree.getPathForLocation(e.getX(), e.getY());
    if (clickedPath == null)
        return;
    DefaultMutableTreeNode node = (DefaultMutableTreeNode) clickedPath.getLastPathComponent();
    Object clickedObject = node.getUserObject();
    if (clickedObject instanceof RawDataFile) {
        RawDataFile clickedFile = (RawDataFile) clickedObject;
        TICVisualizerModule.setupNewTICVisualizer(clickedFile);
    }
    if (clickedObject instanceof PeakList) {
        PeakList clickedPeakList = (PeakList) clickedObject;
        PeakListTableModule.showNewPeakListVisualizerWindow(clickedPeakList);
    }
    if (clickedObject instanceof Scan) {
        Scan clickedScan = (Scan) clickedObject;
        SpectraVisualizerModule.showNewSpectrumWindow(clickedScan.getDataFile(), clickedScan.getScanNumber());
    }
    if (clickedObject instanceof MassList) {
        MassList clickedMassList = (MassList) clickedObject;
        Scan clickedScan = clickedMassList.getScan();
        SpectraVisualizerWindow window = SpectraVisualizerModule.showNewSpectrumWindow(clickedScan.getDataFile(), clickedScan.getScanNumber());
        MassListDataSet dataset = new MassListDataSet(clickedMassList);
        window.addDataSet(dataset, Color.green);
    }
    if (clickedObject instanceof PeakListRow) {
        PeakListRow clickedPeak = (PeakListRow) clickedObject;
        PeakSummaryVisualizerModule.showNewPeakSummaryWindow(clickedPeak);
    }
}