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

Example 1 with IsotopePattern

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

the class SimplePeakListRow method getBestIsotopePattern.

/**
 * Returns the highest isotope pattern of a peak in this row
 */
@Override
public IsotopePattern getBestIsotopePattern() {
    Feature[] peaks = getPeaks();
    Arrays.sort(peaks, new PeakSorter(SortingProperty.Height, SortingDirection.Descending));
    for (Feature peak : peaks) {
        IsotopePattern ip = peak.getIsotopePattern();
        if (ip != null)
            return ip;
    }
    return null;
}

Example 2 with IsotopePattern

use of net.sf.mzmine.datamodel.IsotopePattern 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 IsotopePattern

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

the class SQLExportTask method exportPeakListRow.

private void exportPeakListRow(PeakListRow row) throws SQLException {
    // Cancel?
    if (isCanceled()) {
        return;
    }
    // Value for looping through raw data files
    boolean loopDataFiles = false;
    StringBuilder sql = new StringBuilder();
    sql.append("INSERT INTO ");
    sql.append(tableName);
    sql.append(" (");
    for (int i = 0; i < exportColumns.getRowCount(); i++) {
        sql.append(exportColumns.getValueAt(i, 0));
        if (i < exportColumns.getRowCount() - 1)
            sql.append(",");
    }
    sql.append(" ) VALUES (");
    for (int i = 0; i < exportColumns.getRowCount(); i++) {
        sql.append("?");
        if (i < exportColumns.getRowCount() - 1)
            sql.append(",");
    }
    sql.append(")");
    PreparedStatement statement = dbConnection.prepareStatement(sql.toString());
    if (row == null) {
        for (int i = 0; i < exportColumns.getRowCount(); i++) {
            SQLExportDataType dataType = (SQLExportDataType) exportColumns.getValueAt(i, 1);
            String dataValue = (String) exportColumns.getValueAt(i, 2);
            switch(dataType) {
                case CONSTANT:
                    statement.setString(i + 1, dataValue);
                    break;
                case RAWFILE:
                    RawDataFile[] rawdatafiles = peakList.getRawDataFiles();
                    statement.setString(i + 1, rawdatafiles[0].getName());
                    break;
                default:
                    statement.setString(i + 1, null);
                    break;
            }
        }
        statement.executeUpdate();
    } else {
        for (RawDataFile rawDataFile : row.getRawDataFiles()) {
            Feature peak = row.getPeak(rawDataFile);
            for (int i = 0; i < exportColumns.getRowCount(); i++) {
                SQLExportDataType dataType = (SQLExportDataType) exportColumns.getValueAt(i, 1);
                String dataValue = (String) exportColumns.getValueAt(i, 2);
                switch(dataType) {
                    case CONSTANT:
                        statement.setString(i + 1, dataValue);
                        break;
                    case MZ:
                        statement.setDouble(i + 1, row.getAverageMZ());
                        break;
                    case RT:
                        statement.setDouble(i + 1, row.getAverageRT());
                        break;
                    case ID:
                        statement.setInt(i + 1, row.getID());
                        break;
                    case PEAKCHARGE:
                        statement.setDouble(i + 1, peak.getCharge());
                        loopDataFiles = true;
                        break;
                    case PEAKDURATION:
                        statement.setDouble(i + 1, RangeUtils.rangeLength(peak.getRawDataPointsRTRange()));
                        loopDataFiles = true;
                        break;
                    case PEAKSTATUS:
                        statement.setString(i + 1, peak.getFeatureStatus().name());
                        loopDataFiles = true;
                        break;
                    case PEAKMZ:
                        statement.setDouble(i + 1, peak.getMZ());
                        loopDataFiles = true;
                        break;
                    case PEAKRT:
                        statement.setDouble(i + 1, peak.getRT());
                        loopDataFiles = true;
                        break;
                    case PEAKRT_START:
                        statement.setDouble(i + 1, peak.getRawDataPointsRTRange().lowerEndpoint());
                        loopDataFiles = true;
                        break;
                    case PEAKRT_END:
                        statement.setDouble(i + 1, peak.getRawDataPointsRTRange().upperEndpoint());
                        loopDataFiles = true;
                        break;
                    case PEAKHEIGHT:
                        statement.setDouble(i + 1, peak.getHeight());
                        loopDataFiles = true;
                        break;
                    case PEAKAREA:
                        statement.setDouble(i + 1, peak.getArea());
                        loopDataFiles = true;
                        break;
                    case DATAPOINTS:
                        statement.setDouble(i + 1, peak.getScanNumbers().length);
                        loopDataFiles = true;
                        break;
                    case FWHM:
                        statement.setDouble(i + 1, peak.getFWHM());
                        loopDataFiles = true;
                        break;
                    case TAILINGFACTOR:
                        statement.setDouble(i + 1, peak.getTailingFactor());
                        loopDataFiles = true;
                        break;
                    case ASYMMETRYFACTOR:
                        statement.setDouble(i + 1, peak.getAsymmetryFactor());
                        loopDataFiles = true;
                        break;
                    case RAWFILE:
                        statement.setString(i + 1, rawDataFile.getName());
                        loopDataFiles = true;
                        break;
                    case HEIGHT:
                        statement.setDouble(i + 1, row.getAverageHeight());
                        break;
                    case AREA:
                        statement.setDouble(i + 1, row.getAverageArea());
                        break;
                    case COMMENT:
                        statement.setString(i + 1, row.getComment());
                        break;
                    case IDENTITY:
                        PeakIdentity id = row.getPreferredPeakIdentity();
                        if (id != null) {
                            statement.setString(i + 1, id.getName());
                        } else {
                            statement.setNull(i + 1, Types.VARCHAR);
                        }
                        break;
                    case ISOTOPEPATTERN:
                        IsotopePattern isotopes = row.getBestIsotopePattern();
                        if (isotopes == null) {
                            statement.setNull(i + 1, Types.BLOB);
                            break;
                        }
                        DataPoint[] dataPoints = isotopes.getDataPoints();
                        byte[] bytes = ScanUtils.encodeDataPointsToBytes(dataPoints);
                        ByteArrayInputStream is = new ByteArrayInputStream(bytes);
                        statement.setBlob(i + 1, is);
                        break;
                    case MSMS:
                        int msmsScanNum = row.getBestPeak().getMostIntenseFragmentScanNumber();
                        // Check if there is any MS/MS scan
                        if (msmsScanNum <= 0) {
                            statement.setNull(i + 1, Types.BLOB);
                            break;
                        }
                        RawDataFile dataFile = row.getBestPeak().getDataFile();
                        Scan msmsScan = dataFile.getScan(msmsScanNum);
                        MassList msmsMassList = msmsScan.getMassList(dataValue);
                        // Check if there is a masslist for the scan
                        if (msmsMassList == null) {
                            statement.setNull(i + 1, Types.BLOB);
                            break;
                        }
                        dataPoints = msmsMassList.getDataPoints();
                        bytes = ScanUtils.encodeDataPointsToBytes(dataPoints);
                        is = new ByteArrayInputStream(bytes);
                        statement.setBlob(i + 1, is);
                        break;
                    default:
                        break;
                }
            }
            statement.executeUpdate();
            // data files in feature list
            if (!loopDataFiles) {
                break;
            }
        }
    }
}

Example 4 with IsotopePattern

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

the class RTScore method calculateScore.

public double calculateScore(AlignmentPath path, PeakListRow peak, ParameterSet parameters) {
    try {
        rtTolerance = parameters.getParameter(PathAlignerParameters.RTTolerance).getValue();
        mzTolerance = parameters.getParameter(PathAlignerParameters.MZTolerance).getValue();
        Range<Double> rtRange = rtTolerance.getToleranceRange(path.getRT());
        Range<Double> mzRange = mzTolerance.getToleranceRange(path.getMZ());
        if (!rtRange.contains(peak.getAverageRT()) || !mzRange.contains(peak.getAverageMZ())) {
            return WORST_SCORE;
        }
        double mzDiff = Math.abs(path.getMZ() - peak.getAverageMZ());
        double rtDiff = Math.abs(path.getRT() - peak.getAverageRT());
        double score = ((mzDiff / (RangeUtils.rangeLength(mzRange) / 2.0))) + ((rtDiff / (RangeUtils.rangeLength(rtRange) / 2.0)));
        if (parameters.getParameter(PathAlignerParameters.SameChargeRequired).getValue()) {
            if (!PeakUtils.compareChargeState(path.convertToAlignmentRow(0), peak)) {
                return WORST_SCORE;
            }
        }
        if (parameters.getParameter(PathAlignerParameters.SameIDRequired).getValue()) {
            if (!PeakUtils.compareIdentities(path.convertToAlignmentRow(0), peak)) {
                return WORST_SCORE;
            }
        }
        if (parameters.getParameter(PathAlignerParameters.compareIsotopePattern).getValue()) {
            IsotopePattern ip1 = path.convertToAlignmentRow(0).getBestIsotopePattern();
            IsotopePattern ip2 = peak.getBestIsotopePattern();
            if ((ip1 != null) && (ip2 != null)) {
                ParameterSet isotopeParams = parameters.getParameter(PathAlignerParameters.compareIsotopePattern).getEmbeddedParameters();
                if (!IsotopePatternScoreCalculator.checkMatch(ip1, ip2, isotopeParams)) {
                    return WORST_SCORE;
                }
            }
        }
        return score;
    } catch (NullPointerException e) {
        e.printStackTrace();
        return WORST_SCORE;
    }
}

Example 5 with IsotopePattern

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

the class DPPIsotopeGrouperTask method compressIsotopeDataSets.

/**
 * This method generates a single IsotopesDataSet from all detected isotope patterns in the
 * results.
 *
 * @param dataPoints
 * @return
 */
private IsotopesDataSet compressIsotopeDataSets(ProcessedDataPoint[] dataPoints) {
    List<IsotopePattern> list = new ArrayList<>();
    for (ProcessedDataPoint dp : dataPoints) {
        if (dp.resultTypeExists(ResultType.ISOTOPEPATTERN)) {
            list.add(((DPPIsotopePatternResult) dp.getFirstResultByType(ResultType.ISOTOPEPATTERN)).getValue());
        }
    }
    if (list.isEmpty())
        return null;
    List<DataPoint> dpList = new ArrayList<>();
    for (IsotopePattern pattern : list) {
        for (DataPoint dp : pattern.getDataPoints()) dpList.add(dp);
    }
    if (dpList.isEmpty())
        return null;
    IsotopePattern full = new SimpleIsotopePattern(dpList.toArray(new DataPoint[0]), IsotopePatternStatus.DETECTED, "Isotope patterns");
    return new IsotopesDataSet(full);
}