Examples with MassDetector net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetector used on opensource projects

Example 1 with MassDetector

use of net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetector in project mzmine2 by mzmine.

the class SpectraIdentificationLipidSearchTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    // create mass list for scan
    DataPoint[] massList = null;
    ArrayList<DataPoint> massListAnnotated = new ArrayList<>();
    MassDetector massDetector = null;
    ArrayList<String> allCompoundIDs = new ArrayList<>();
    // Create a new mass list for MS/MS scan. Check if sprectrum is profile or centroid mode
    if (currentScan.getSpectrumType() == MassSpectrumType.CENTROIDED) {
        massDetector = new CentroidMassDetector();
        CentroidMassDetectorParameters parameters = new CentroidMassDetectorParameters();
        CentroidMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    } else {
        massDetector = new ExactMassDetector();
        ExactMassDetectorParameters parameters = new ExactMassDetectorParameters();
        ExactMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    }
    totalSteps = massList.length;
    // loop through every peak in mass list
    if (getStatus() != TaskStatus.PROCESSING) {
        return;
    }
    // Check if lipids should be modified
    if (searchForModifications == true) {
        lipidModificationMasses = getLipidModificationMasses(lipidModification);
    }
    // Calculate how many possible lipids we will try
    totalSteps = (((maxChainLength - minChainLength + 1) * (maxDoubleBonds - minDoubleBonds + 1)) * selectedLipids.length);
    // Combine Strings
    String annotation = "";
    // Try all combinations of fatty acid lengths and double bonds
    for (int j = 0; j < selectedLipids.length; j++) {
        int numberOfAcylChains = selectedLipids[j].getNumberOfAcylChains();
        int numberOfAlkylChains = selectedLipids[j].getNumberofAlkyChains();
        for (int chainLength = minChainLength; chainLength <= maxChainLength; chainLength++) {
            for (int chainDoubleBonds = minDoubleBonds; chainDoubleBonds <= maxDoubleBonds; chainDoubleBonds++) {
                for (int i = 0; i < massList.length; i++) {
                    searchedMass = massList[i].getMZ();
                    // Task canceled?
                    if (isCanceled())
                        return;
                    // than minimal length, skip this lipid
                    if (((chainLength > 0) && (chainLength < minChainLength))) {
                        continue;
                    }
                    // doesn't make sense, so let's skip such lipids
                    if (((chainDoubleBonds > 0) && (chainDoubleBonds > chainLength - 1))) {
                        continue;
                    }
                    // Prepare a lipid instance
                    LipidIdentity lipidChain = new LipidIdentity(selectedLipids[j], chainLength, chainDoubleBonds, numberOfAcylChains, numberOfAlkylChains);
                    annotation = findPossibleLipid(lipidChain, searchedMass);
                    if (annotation != "") {
                        allCompoundIDs.add(annotation);
                        massListAnnotated.add(massList[i]);
                    }
                    annotation = findPossibleLipidModification(lipidChain, searchedMass);
                    if (annotation != "") {
                        allCompoundIDs.add(annotation);
                        massListAnnotated.add(massList[i]);
                    }
                }
                finishedSteps++;
            }
        }
    }
    // new mass list
    DataPoint[] annotatedMassList = new DataPoint[massListAnnotated.size()];
    massListAnnotated.toArray(annotatedMassList);
    String[] annotations = new String[annotatedMassList.length];
    allCompoundIDs.toArray(annotations);
    DataPointsDataSet detectedCompoundsDataset = new DataPointsDataSet("Detected compounds", annotatedMassList);
    // Add label generator for the dataset
    SpectraDatabaseSearchLabelGenerator labelGenerator = new SpectraDatabaseSearchLabelGenerator(annotations, spectraPlot);
    spectraPlot.addDataSet(detectedCompoundsDataset, Color.orange, true, labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setSeriesItemLabelGenerator(spectraPlot.getXYPlot().getSeriesCount(), labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setDefaultPositiveItemLabelPosition(new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.TOP_LEFT, TextAnchor.BOTTOM_CENTER, 0.0), true);
    setStatus(TaskStatus.FINISHED);
}

Example 2 with MassDetector

use of net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetector in project mzmine2 by mzmine.

the class DPPMassDetectionTask method run.

@Override
public void run() {
    if (!checkParameterSet() || !checkValues()) {
        setStatus(TaskStatus.ERROR);
        return;
    }
    if (getStatus() == TaskStatus.CANCELED) {
        return;
    }
    setStatus(TaskStatus.PROCESSING);
    MassDetector detector = massDetector.getModule();
    DataPoint[] masses = detector.getMassValues(getDataPoints(), massDetector.getParameterSet());
    if (masses == null || masses.length <= 0) {
        Logger.info("Data point/Spectra processing: No masses were detected with the given parameters.");
        setStatus(TaskStatus.CANCELED);
        return;
    }
    ProcessedDataPoint[] dp = ProcessedDataPoint.convert(masses);
    currentIndex = dataPoints.length;
    setResults(dp);
    setStatus(TaskStatus.FINISHED);
}

Example 3 with MassDetector

use of net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetector in project mzmine2 by mzmine.

the class SpectraIdentificationOnlineDatabaseTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    // create mass list for scan
    DataPoint[] massList = null;
    ArrayList<DataPoint> massListAnnotated = new ArrayList<>();
    MassDetector massDetector = null;
    ArrayList<String> allCompoundIDs = new ArrayList<>();
    // Create a new mass list for MS/MS scan. Check if sprectrum is profile or centroid mode
    if (currentScan.getSpectrumType() == MassSpectrumType.CENTROIDED) {
        massDetector = new CentroidMassDetector();
        CentroidMassDetectorParameters parameters = new CentroidMassDetectorParameters();
        CentroidMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    } else {
        massDetector = new ExactMassDetector();
        ExactMassDetectorParameters parameters = new ExactMassDetectorParameters();
        ExactMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    }
    numItems = massList.length;
    for (int i = 0; i < massList.length; i++) {
        // loop through every peak in mass list
        if (getStatus() != TaskStatus.PROCESSING) {
            return;
        }
        searchedMass = massList[i].getMZ() - ionType.getAddedMass();
        try {
            // find candidate compounds
            String[] compoundIDs = gateway.findCompounds(searchedMass, mzTolerance, 1, db.getParameterSet());
            // Combine strings
            String annotation = "";
            // max number of compounds to top three for visualization
            int counter = 0;
            for (int j = 0; !isCanceled() && j < compoundIDs.length; j++) {
                final DBCompound compound = gateway.getCompound(compoundIDs[j], db.getParameterSet());
                // In case we failed to retrieve data, skip this compound
                if (compound == null)
                    continue;
                if (counter < 3) {
                    int number = counter + 1;
                    annotation = annotation + " " + number + ". " + compound.getName();
                    counter++;
                }
            }
            if (annotation != "") {
                allCompoundIDs.add(annotation);
                massListAnnotated.add(massList[i]);
            }
        } catch (Exception e) {
            e.printStackTrace();
            logger.log(Level.WARNING, "Could not connect to " + db, e);
            setStatus(TaskStatus.ERROR);
            setErrorMessage("Could not connect to " + db + ": " + ExceptionUtils.exceptionToString(e));
            return;
        }
        finishedItems++;
    }
    // new mass list
    DataPoint[] annotatedMassList = new DataPoint[massListAnnotated.size()];
    massListAnnotated.toArray(annotatedMassList);
    String[] annotations = new String[annotatedMassList.length];
    allCompoundIDs.toArray(annotations);
    DataPointsDataSet detectedCompoundsDataset = new DataPointsDataSet("Detected compounds", annotatedMassList);
    // Add label generator for the dataset
    SpectraDatabaseSearchLabelGenerator labelGenerator = new SpectraDatabaseSearchLabelGenerator(annotations, spectraPlot);
    spectraPlot.addDataSet(detectedCompoundsDataset, Color.orange, true, labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setSeriesItemLabelGenerator(spectraPlot.getXYPlot().getSeriesCount(), labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setDefaultPositiveItemLabelPosition(new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.TOP_LEFT, TextAnchor.BOTTOM_CENTER, 0.0), true);
    setStatus(TaskStatus.FINISHED);
}

Example 4 with MassDetector

use of net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetector in project mzmine2 by mzmine.

the class SpectraIdentificationSumFormulaTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.finest("Starting search for formulas for " + massRange + " Da");
    // create mass list for scan
    DataPoint[] massList = null;
    ArrayList<DataPoint> massListAnnotated = new ArrayList<>();
    MassDetector massDetector = null;
    ArrayList<String> allCompoundIDs = new ArrayList<>();
    // Create a new mass list for MS/MS scan. Check if sprectrum is profile or centroid mode
    if (currentScan.getSpectrumType() == MassSpectrumType.CENTROIDED) {
        massDetector = new CentroidMassDetector();
        CentroidMassDetectorParameters parameters = new CentroidMassDetectorParameters();
        CentroidMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    } else {
        massDetector = new ExactMassDetector();
        ExactMassDetectorParameters parameters = new ExactMassDetectorParameters();
        ExactMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    }
    numItems = massList.length;
    // loop through every peak in mass list
    if (getStatus() != TaskStatus.PROCESSING) {
        return;
    }
    IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
    for (int i = 0; i < massList.length; i++) {
        massRange = mzTolerance.getToleranceRange((massList[i].getMZ() - ionType.getAddedMass()) / charge);
        generator = new MolecularFormulaGenerator(builder, massRange.lowerEndpoint(), massRange.upperEndpoint(), elementCounts);
        IMolecularFormula cdkFormula;
        String annotation = "";
        // create a map to store ResultFormula and relative mass deviation for sorting
        Map<Double, String> possibleFormulas = new TreeMap<>();
        while ((cdkFormula = generator.getNextFormula()) != null) {
            if (isCanceled())
                return;
            // Mass is ok, so test other constraints
            if (checkConstraints(cdkFormula) == true) {
                String formula = MolecularFormulaManipulator.getString(cdkFormula);
                // calc rel mass deviation
                Double relMassDev = ((((// 
                massList[i].getMZ() - ionType.getAddedMass()) / // 
                charge) - (// 
                FormulaUtils.calculateExactMass(MolecularFormulaManipulator.getString(cdkFormula))) / charge) / ((// 
                massList[i].getMZ() - ionType.getAddedMass()) / charge)) * 1000000;
                // write to map
                possibleFormulas.put(relMassDev, formula);
            }
        }
        Map<Double, String> treeMap = new TreeMap<>((Comparator<Double>) (o1, o2) -> Double.compare(Math.abs(o1), Math.abs(o2)));
        treeMap.putAll(possibleFormulas);
        // get top 3
        int ctr = 0;
        for (Map.Entry<Double, String> entry : treeMap.entrySet()) {
            int number = ctr + 1;
            if (ctr > 2)
                break;
            annotation = annotation + number + ". " + entry.getValue() + " Δ " + NumberFormat.getInstance().format(entry.getKey()) + " ppm; ";
            ctr++;
            if (isCanceled())
                return;
        }
        if (annotation != "") {
            allCompoundIDs.add(annotation);
            massListAnnotated.add(massList[i]);
        }
        logger.finest("Finished formula search for " + massRange + " m/z, found " + foundFormulas + " formulas");
    }
    // new mass list
    DataPoint[] annotatedMassList = new DataPoint[massListAnnotated.size()];
    massListAnnotated.toArray(annotatedMassList);
    String[] annotations = new String[annotatedMassList.length];
    allCompoundIDs.toArray(annotations);
    DataPointsDataSet detectedCompoundsDataset = new DataPointsDataSet("Detected compounds", annotatedMassList);
    // Add label generator for the dataset
    SpectraDatabaseSearchLabelGenerator labelGenerator = new SpectraDatabaseSearchLabelGenerator(annotations, spectraPlot);
    spectraPlot.addDataSet(detectedCompoundsDataset, Color.orange, true, labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setSeriesItemLabelGenerator(spectraPlot.getXYPlot().getSeriesCount(), labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setDefaultPositiveItemLabelPosition(new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.TOP_LEFT, TextAnchor.BOTTOM_CENTER, 0.0), true);
    setStatus(TaskStatus.FINISHED);
}

Example 5 with MassDetector

use of net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetector in project mzmine2 by mzmine.

the class SpectraIdentificationCustomDatabaseTask method run.

/**
 * @see java.lang.Runnable#run()
 */
@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    // create mass list for scan
    DataPoint[] massList = null;
    ArrayList<DataPoint> massListAnnotated = new ArrayList<>();
    MassDetector massDetector = null;
    ArrayList<String> allCompoundIDs = new ArrayList<>();
    // Create a new mass list for MS/MS scan. Check if sprectrum is profile or centroid mode
    if (currentScan.getSpectrumType() == MassSpectrumType.CENTROIDED) {
        massDetector = new CentroidMassDetector();
        CentroidMassDetectorParameters parameters = new CentroidMassDetectorParameters();
        CentroidMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    } else {
        massDetector = new ExactMassDetector();
        ExactMassDetectorParameters parameters = new ExactMassDetectorParameters();
        ExactMassDetectorParameters.noiseLevel.setValue(noiseLevel);
        massList = massDetector.getMassValues(currentScan.getDataPoints(), parameters);
    }
    numItems = massList.length;
    // load custom database
    try {
        // read database contents in memory
        FileReader dbFileReader = new FileReader(dataBaseFile);
        databaseValues = CSVParser.parse(dbFileReader, fieldSeparator.charAt(0));
        if (ignoreFirstLine)
            finishedLines++;
        for (; finishedLines < databaseValues.length; finishedLines++) {
            if (isCanceled()) {
                dbFileReader.close();
                return;
            }
            int numOfColumns = Math.min(fieldOrder.length, databaseValues[finishedLines].length);
            String lineName = null;
            double lineMZ = 0;
            for (int i = 0; i < numOfColumns; i++) {
                if (fieldOrder[i] == FieldItem.FIELD_NAME)
                    lineName = databaseValues[finishedLines][i].toString();
                if (fieldOrder[i] == FieldItem.FIELD_MZ)
                    lineMZ = Double.parseDouble(databaseValues[finishedLines][i].toString());
            }
            for (int i = 0; i < massList.length; i++) {
                // loop through every peak in mass list
                if (getStatus() != TaskStatus.PROCESSING) {
                    return;
                }
                double searchedMass = massList[i].getMZ();
                Range<Double> mzRange = mzTolerance.getToleranceRange(searchedMass);
                boolean mzMatches = (lineMZ == 0d) || mzRange.contains(lineMZ);
                String annotation = "";
                if (mzMatches) {
                    // calc rel mass deviation
                    double relMassDev = ((searchedMass - lineMZ) / searchedMass) * 1000000;
                    logger.finest("Found compound " + lineName + " m/z " + NumberFormat.getInstance().format(searchedMass) + " Δ " + NumberFormat.getInstance().format(relMassDev) + " ppm");
                    annotation = lineName + " Δ " + NumberFormat.getInstance().format(relMassDev) + " ppm";
                }
                if (annotation != "") {
                    allCompoundIDs.add(annotation);
                    massListAnnotated.add(massList[i]);
                }
            }
            finishedLines++;
        }
        // close the file reader
        dbFileReader.close();
    } catch (Exception e) {
        logger.log(Level.WARNING, "Could not read file " + dataBaseFile, e);
        setStatus(TaskStatus.ERROR);
        setErrorMessage(e.toString());
        return;
    }
    // new mass list
    DataPoint[] annotatedMassList = new DataPoint[massListAnnotated.size()];
    massListAnnotated.toArray(annotatedMassList);
    String[] annotations = new String[annotatedMassList.length];
    allCompoundIDs.toArray(annotations);
    DataPointsDataSet detectedCompoundsDataset = new DataPointsDataSet("Detected compounds", annotatedMassList);
    // Add label generator for the dataset
    SpectraDatabaseSearchLabelGenerator labelGenerator = new SpectraDatabaseSearchLabelGenerator(annotations, spectraPlot);
    spectraPlot.addDataSet(detectedCompoundsDataset, Color.orange, true, labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setSeriesItemLabelGenerator(spectraPlot.getXYPlot().getSeriesCount(), labelGenerator);
    spectraPlot.getXYPlot().getRenderer().setDefaultPositiveItemLabelPosition(new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.TOP_LEFT, TextAnchor.BOTTOM_CENTER, 0.0), true);
    setStatus(TaskStatus.FINISHED);
}