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

Example 1 with SimpleIsotopePattern

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

the class ADAP3DecompositionV1_5Task method decomposePeaks.

private PeakList decomposePeaks(PeakList peakList) throws CloneNotSupportedException, IOException {
    RawDataFile dataFile = peakList.getRawDataFile(0);
    // Create new feature list.
    final PeakList resolvedPeakList = new SimplePeakList(peakList + " " + parameters.getParameter(ADAP3DecompositionV1_5Parameters.SUFFIX).getValue(), dataFile);
    // Load previous applied methods.
    for (final PeakList.PeakListAppliedMethod method : peakList.getAppliedMethods()) {
        resolvedPeakList.addDescriptionOfAppliedTask(method);
    }
    // Add task description to feature list.
    resolvedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peak deconvolution by ADAP-3", parameters));
    // Collect peak information
    List<Peak> peaks = getPeaks(peakList, this.parameters.getParameter(ADAP3DecompositionV1_5Parameters.EDGE_TO_HEIGHT_RATIO).getValue(), this.parameters.getParameter(ADAP3DecompositionV1_5Parameters.DELTA_TO_HEIGHT_RATIO).getValue());
    // Find components (a.k.a. clusters of peaks with fragmentation spectra)
    List<Component> components = getComponents(peaks);
    // Create PeakListRow for each components
    List<PeakListRow> newPeakListRows = new ArrayList<>();
    int rowID = 0;
    for (final Component component : components) {
        if (component.getSpectrum().isEmpty())
            continue;
        PeakListRow row = new SimplePeakListRow(++rowID);
        // Add the reference peak
        PeakListRow refPeakRow = originalPeakList.getRow(component.getBestPeak().getInfo().peakID);
        Feature refPeak = new SimpleFeature(refPeakRow.getBestPeak());
        // Add spectrum
        List<DataPoint> dataPoints = new ArrayList<>();
        for (Map.Entry<Double, Double> entry : component.getSpectrum().entrySet()) {
            dataPoints.add(new SimpleDataPoint(entry.getKey(), entry.getValue()));
        }
        refPeak.setIsotopePattern(new SimpleIsotopePattern(dataPoints.toArray(new DataPoint[dataPoints.size()]), IsotopePattern.IsotopePatternStatus.PREDICTED, "Spectrum"));
        row.addPeak(dataFile, refPeak);
        // Add PeakInformation
        if (refPeakRow.getPeakInformation() == null) {
            SimplePeakInformation information = new SimplePeakInformation(new HashMap<>(refPeakRow.getPeakInformation().getAllProperties()));
            row.setPeakInformation(information);
        }
        // Set row properties
        row.setAverageMZ(refPeakRow.getAverageMZ());
        row.setAverageRT(refPeakRow.getAverageRT());
        // resolvedPeakList.addRow(row);
        newPeakListRows.add(row);
    }
    // ------------------------------------
    // Sort new peak rows by retention time
    // ------------------------------------
    Collections.sort(newPeakListRows, new Comparator<PeakListRow>() {

        @Override
        public int compare(PeakListRow row1, PeakListRow row2) {
            double retTime1 = row1.getAverageRT();
            double retTime2 = row2.getAverageRT();
            return Double.compare(retTime1, retTime2);
        }
    });
    for (PeakListRow row : newPeakListRows) resolvedPeakList.addRow(row);
    return resolvedPeakList;
}

Example 2 with SimpleIsotopePattern

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

the class IsotopePeakScannerTask method run.

@Override
public void run() {
    if (!checkParameters())
        return;
    setStatus(TaskStatus.PROCESSING);
    totalRows = peakList.getNumberOfRows();
    double[][] diff = setUpDiffAutoCarbon();
    if (diff == null) {
        message = "ERROR: could not set up diff.";
        setStatus(TaskStatus.ERROR);
        return;
    }
    logger.info("diff.length: " + diff.length);
    logger.info("maxPatternIndex: " + maxPatternIndex);
    logger.info("maxPatternSize: " + maxPatternSize);
    // get all rows and sort by m/z
    PeakListRow[] rows = peakList.getRows();
    Arrays.sort(rows, new PeakListRowSorter(SortingProperty.MZ, SortingDirection.Ascending));
    PeakListHandler plh = new PeakListHandler();
    plh.setUp(peakList);
    resultPeakList = new SimplePeakList(peakList.getName() + suffix, peakList.getRawDataFiles());
    PeakListHandler resultMap = new PeakListHandler();
    for (int i = 0; i < totalRows; i++) {
        // i will represent the index of the row in peakList
        if (rows[i].getPeakIdentities().length > 0) {
            finishedRows++;
            continue;
        }
        message = "Row " + i + "/" + totalRows;
        // now get all peaks that lie within RT and maxIsotopeMassRange: pL[index].mz ->
        // pL[index].mz+maxMass
        ArrayList<PeakListRow> groupedPeaks = groupPeaks(rows, i, diff[maxPatternIndex][diff[maxPatternIndex].length - 1]);
        if (groupedPeaks.size() < 2) {
            finishedRows++;
            continue;
        }
        // else
        // logger.info("groupedPeaks.size > 2 in row: " + i + " size: " +
        // groupedPeaks.size());
        // this will store row
        ResultBuffer[][] resultBuffer = new ResultBuffer[diff.length][];
        for (int p = 0; p < diff.length; p++) {
            // resultBuffer[i] index will represent Isotope[i] (if
            // numAtoms = 0)
            resultBuffer[p] = new ResultBuffer[diff[p].length];
            for (int k = 0; k < diff[p].length; k++) // [p][0] will be the isotope with lowest mass#
            resultBuffer[p][k] = new ResultBuffer();
        }
        // of all features with fitting rt
        // and mz
        boolean[] trueBuffers = new boolean[diff.length];
        Arrays.fill(trueBuffers, false);
        for (// go through all possible peaks
        int j = 0; // go through all possible peaks
        j < groupedPeaks.size(); // go through all possible peaks
        j++) {
            for (int p = 0; p < diff.length; p++) {
                for (// check for each peak if it is a possible
                int k = 0; // check for each peak if it is a possible
                k < diff[p].length; // check for each peak if it is a possible
                k++) // feature
                // for
                // every diff[](isotope)
                {
                    // p = pattern index for autoCarbon
                    if (mzTolerance.checkWithinTolerance(groupedPeaks.get(0).getAverageMZ() + diff[p][k], groupedPeaks.get(j).getAverageMZ())) {
                        // this will automatically add groupedPeaks[0] to the list -> isotope with
                        // lowest mass
                        // +1 result for isotope k
                        resultBuffer[p][k].addFound();
                        // row in groupedPeaks[]
                        resultBuffer[p][k].addRow(j);
                        resultBuffer[p][k].addID(groupedPeaks.get(j).getID());
                    }
                }
            }
        }
        boolean foundOne = false;
        for (int p = 0; p < diff.length; p++) if (checkIfAllTrue(resultBuffer[p])) {
            // this means that for every isotope we expected to
            // find,
            // we found one or more possible features
            foundOne = true;
            trueBuffers[p] = true;
        // logger.info("Row: " + i + " filled buffer[" + p +"]");
        }
        if (!foundOne) {
            finishedRows++;
            continue;
        }
        Candidates[] candidates = new Candidates[diff.length];
        for (int p = 0; p < diff.length; p++) candidates[p] = new Candidates(diff[p].length, minHeight, mzTolerance, pattern[p], massListName, plh, ratingType);
        for (int p = 0; p < diff.length; p++) {
            if (!trueBuffers[p])
                continue;
            for (// reminder: resultBuffer.length =
            int k = 0; // reminder: resultBuffer.length =
            k < resultBuffer[p].length; // reminder: resultBuffer.length =
            k++) // diff.length
            {
                for (int l = 0; l < resultBuffer[p][k].getFoundCount(); l++) {
                    // k represents index resultBuffer[k] and thereby the isotope number
                    // l represents the number of results in resultBuffer[k]
                    candidates[p].checkForBetterRating(k, groupedPeaks.get(0), groupedPeaks.get(resultBuffer[p][k].getRow(l)), minRating, checkIntensity);
                }
            }
        }
        foundOne = false;
        boolean[] trueCandidates = new boolean[diff.length];
        Arrays.fill(trueCandidates, false);
        for (int p = 0; p < diff.length; p++) {
            if (trueBuffers[p] && checkIfAllTrue(candidates[p].getCandidates())) {
                trueCandidates[p] = true;
                foundOne = true;
            // logger.info("Row: " + i + " filled candidates[" + p + "]");
            }
        }
        if (!foundOne) {
            finishedRows++;
            // jump to next i
            continue;
        }
        // find best result now, first we have to calc avg ratings if specified by user
        int bestPatternIndex = 0;
        double bestRating = 0.0;
        for (int p = 0; p < diff.length; p++) {
            if (!trueCandidates[p])
                continue;
            if (accurateAvgIntensity)
                candidates[p].calcAvgRatings();
            if (accurateAvgIntensity && candidates[p].getAvgAccAvgRating() > bestRating) {
                bestPatternIndex = p;
                bestRating = candidates[p].getAvgAccAvgRating();
            } else if (!accurateAvgIntensity && candidates[p].getSimpleAvgRating() > bestRating) {
                bestPatternIndex = p;
                bestRating = candidates[p].getSimpleAvgRating();
            }
        }
        if (!checkIfAllTrue(candidates[bestPatternIndex].getCandidates())) {
            logger.warning("We were about to add candidates with null pointers.\nThis was no valid result. Continueing.");
            continue;
        }
        // TODO: this shouldnt be needed, fix the bug that causes the crash later on.
        // this happens occasionally if the user wants to do accurate average but does not filter
        // by RT. then possible isotope peaks are found, although they are not detected at the same
        // time. This will result in the candidates return -1.0 which will sooner or later return a
        // null pointer Fixing this will be done in a future update, but needs a rework of the
        // candidates class.
        // The results you miss by skipping here would have not been valid results anyway, so this
        // is not urgent. Will be nicer though, because of cleaner code.
        // PeakListRow parent = copyPeakRow(peakList.getRow(i));
        boolean allPeaksAddable = true;
        List<PeakListRow> rowBuffer = new ArrayList<PeakListRow>();
        PeakListRow original = getRowFromCandidate(candidates, bestPatternIndex, 0, plh);
        if (original == null)
            continue;
        PeakListRow parent = copyPeakRow(original);
        if (// if we can assign this row multiple times we
        resultMap.containsID(parent.getID()))
            // have to copy the comment, because adding it to
            // the map twice will overwrite the results
            addComment(parent, resultMap.getRowByID(parent.getID()).getComment());
        // ID is added to be able to sort by
        addComment(parent, parent.getID() + "--IS PARENT--");
        if (carbonRange != 1)
            addComment(parent, "BestPattern: " + pattern[bestPatternIndex].getDescription());
        rowBuffer.add(parent);
        DataPoint[] dp = new DataPoint[pattern[bestPatternIndex].getNumberOfDataPoints()];
        if (accurateAvgIntensity) {
            dp[0] = new SimpleDataPoint(parent.getAverageMZ(), candidates[bestPatternIndex].getAvgHeight(0));
        } else {
            dp[0] = new SimpleDataPoint(parent.getAverageMZ(), parent.getAverageHeight());
        }
        for (// we skip k=0 because ==
        int k = 1; // we skip k=0 because ==
        k < candidates[bestPatternIndex].size(); // we skip k=0 because ==
        k++) // groupedPeaks[0]/
        // ==candidates.get(0) which we added before
        {
            PeakListRow originalChild = getRowFromCandidate(candidates, bestPatternIndex, k, plh);
            if (originalChild == null) {
                allPeaksAddable = false;
                continue;
            }
            PeakListRow child = copyPeakRow(originalChild);
            if (accurateAvgIntensity) {
                dp[k] = new SimpleDataPoint(child.getAverageMZ(), candidates[bestPatternIndex].getAvgHeight(k));
            } else {
                dp[k] = new SimpleDataPoint(child.getAverageMZ(), child.getAverageHeight());
            }
            String average = "";
            if (accurateAvgIntensity) {
                average = " AvgRating: " + round(candidates[bestPatternIndex].getAvgRating(k), 3);
            }
            addComment(parent, "Intensity ratios: " + getIntensityRatios(pattern[bestPatternIndex], pattern[bestPatternIndex].getHighestDataPointIndex()));
            if (accurateAvgIntensity)
                addComment(parent, " Avg pattern rating: " + round(candidates[bestPatternIndex].getAvgAccAvgRating(), 3));
            else
                addComment(parent, " pattern rating: " + round(candidates[bestPatternIndex].getSimpleAvgRating(), 3));
            addComment(child, (parent.getID() + "-Parent ID" + " m/z-shift(ppm): " + round(((child.getAverageMZ() - parent.getAverageMZ()) - diff[bestPatternIndex][k]) / child.getAverageMZ() * 1E6, 2) + " I(c)/I(p): " + round(child.getAverageHeight() / plh.getRowByID(candidates[bestPatternIndex].get(pattern[bestPatternIndex].getHighestDataPointIndex()).getCandID()).getAverageHeight(), 2) + " Identity: " + pattern[bestPatternIndex].getIsotopeComposition(k) + " Rating: " + round(candidates[bestPatternIndex].get(k).getRating(), 3) + average));
            rowBuffer.add(child);
        }
        if (!allPeaksAddable)
            continue;
        IsotopePattern resultPattern = new SimpleIsotopePattern(dp, IsotopePatternStatus.DETECTED, element + " monoisotopic mass: " + parent.getAverageMZ());
        parent.getBestPeak().setIsotopePattern(resultPattern);
        for (PeakListRow row : rowBuffer) {
            row.getBestPeak().setIsotopePattern(resultPattern);
            resultMap.addRow(row);
        }
        if (isCanceled())
            return;
        finishedRows++;
    }
    ArrayList<Integer> keys = resultMap.getAllKeys();
    for (int j = 0; j < keys.size(); j++) resultPeakList.addRow(resultMap.getRowByID(keys.get(j)));
    if (resultPeakList.getNumberOfRows() > 1)
        addResultToProject();
    else
        message = "Element not found.";
    setStatus(TaskStatus.FINISHED);
}

Example 3 with SimpleIsotopePattern

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

the class IsotopePatternCalculator method normalizeIsotopePattern.

/**
 * Returns same isotope pattern (same ratios between isotope intensities) with maximum intensity
 * normalized to given intensity
 */
public static IsotopePattern normalizeIsotopePattern(IsotopePattern pattern, double normalizedValue) {
    DataPoint highestIsotope = pattern.getHighestDataPoint();
    DataPoint[] dataPoints = pattern.getDataPoints();
    double maxIntensity = highestIsotope.getIntensity();
    DataPoint[] newDataPoints = new DataPoint[dataPoints.length];
    for (int i = 0; i < dataPoints.length; i++) {
        double mz = dataPoints[i].getMZ();
        double intensity = dataPoints[i].getIntensity() / maxIntensity * normalizedValue;
        newDataPoints[i] = new SimpleDataPoint(mz, intensity);
    }
    if (pattern instanceof ExtendedIsotopePattern && ((ExtendedIsotopePattern) pattern).getIsotopeCompositions() != null)
        return new ExtendedIsotopePattern(newDataPoints, pattern.getStatus(), pattern.getDescription(), ((ExtendedIsotopePattern) pattern).getIsotopeCompositions());
    else
        return new SimpleIsotopePattern(newDataPoints, pattern.getStatus(), pattern.getDescription());
}

Example 4 with SimpleIsotopePattern

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

the class IsotopePatternCalculator method mergeIsotopes.

/**
 * Merges the isotopes falling within the given m/z tolerance. If the m/z difference between the
 * isotopes is smaller than mzTolerance, their intensity is added together and new m/z value is
 * calculated as a weighted average.
 */
public static IsotopePattern mergeIsotopes(IsotopePattern pattern, double mzTolerance) {
    DataPoint[] dataPoints = pattern.getDataPoints().clone();
    String[] newIsotopeComposition = new String[pattern.getNumberOfDataPoints()];
    if (pattern instanceof ExtendedIsotopePattern && ((ExtendedIsotopePattern) pattern).getIsotopeCompositions() != null)
        newIsotopeComposition = ((ExtendedIsotopePattern) pattern).getIsotopeCompositions();
    for (int i = 0; i < dataPoints.length - 1; i++) {
        if (Math.abs(dataPoints[i].getMZ() - dataPoints[i + 1].getMZ()) < mzTolerance) {
            double newIntensity = dataPoints[i].getIntensity() + dataPoints[i + 1].getIntensity();
            double newMZ = (dataPoints[i].getMZ() * dataPoints[i].getIntensity() + dataPoints[i + 1].getMZ() * dataPoints[i + 1].getIntensity()) / newIntensity;
            dataPoints[i + 1] = new SimpleDataPoint(newMZ, newIntensity);
            dataPoints[i] = null;
            if (pattern instanceof ExtendedIsotopePattern && ((ExtendedIsotopePattern) pattern).getIsotopeCompositions() != null) {
                newIsotopeComposition[i + 1] = ((ExtendedIsotopePattern) pattern).getIsotopeComposition(i) + ", " + ((ExtendedIsotopePattern) pattern).getIsotopeComposition(i + 1);
                newIsotopeComposition[i] = null;
            }
        }
    }
    ArrayList<DataPoint> newDataPoints = new ArrayList<DataPoint>();
    for (DataPoint dp : dataPoints) {
        if (dp != null)
            newDataPoints.add(dp);
    }
    if (pattern instanceof ExtendedIsotopePattern && ((ExtendedIsotopePattern) pattern).getIsotopeCompositions() != null) {
        ArrayList<String> newComp = new ArrayList<String>();
        for (String comp : newIsotopeComposition) {
            if (comp != null)
                newComp.add(comp);
        }
        return new ExtendedIsotopePattern(newDataPoints.toArray(new DataPoint[0]), pattern.getStatus(), pattern.getDescription(), newComp.toArray(new String[0]));
    }
    return new SimpleIsotopePattern(newDataPoints.toArray(new DataPoint[0]), pattern.getStatus(), pattern.getDescription());
}

Example 5 with SimpleIsotopePattern

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

the class IsotopePatternCalculator method calculateIsotopePattern.

public static IsotopePattern calculateIsotopePattern(IMolecularFormula cdkFormula, double minAbundance, double mergeWidth, int charge, PolarityType polarity, boolean storeFormula) {
    // TODO: check if the formula is not too big (>100 of a single atom?).
    // if so, just cancel the prediction
    // Set the minimum abundance of isotope
    // TODO: in the CDK minAbundance is now called minIntensity and refers to the relative intensity
    // in the isotope pattern, should change it here, too
    IsotopePatternGenerator generator = new IsotopePatternGenerator(minAbundance);
    generator.setMinResolution(mergeWidth);
    generator.setStoreFormulas(storeFormula);
    org.openscience.cdk.formula.IsotopePattern pattern = generator.getIsotopes(cdkFormula);
    int numOfIsotopes = pattern.getNumberOfIsotopes();
    DataPoint[] dataPoints = new DataPoint[numOfIsotopes];
    String[] isotopeComposition = new String[numOfIsotopes];
    for (int i = 0; i < numOfIsotopes; i++) {
        IsotopeContainer isotope = pattern.getIsotope(i);
        // For each unit of charge, we have to add or remove a mass of a
        // single electron. If the charge is positive, we remove electron
        // mass. If the charge is negative, we add it.
        double mass = isotope.getMass() + (polarity.getSign() * -1 * charge * ELECTRON_MASS);
        if (charge != 0)
            mass /= charge;
        double intensity = isotope.getIntensity();
        dataPoints[i] = new SimpleDataPoint(mass, intensity);
        if (storeFormula)
            isotopeComposition[i] = formatCDKString(isotope.toString());
    }
    String formulaString = MolecularFormulaManipulator.getString(cdkFormula);
    if (storeFormula)
        return new ExtendedIsotopePattern(dataPoints, IsotopePatternStatus.PREDICTED, formulaString, isotopeComposition);
    else
        return new SimpleIsotopePattern(dataPoints, IsotopePatternStatus.PREDICTED, formulaString);
}