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

Example 71 with Feature

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

the class PeakFilterTask method copyPeakRow.

/**
 * Create a copy of a feature list row.
 */
private static PeakListRow copyPeakRow(final PeakListRow row, final boolean[] keepPeak) {
    // Copy the feature list row.
    final PeakListRow newRow = new SimplePeakListRow(row.getID());
    PeakUtils.copyPeakListRowProperties(row, newRow);
    // Copy the peaks.
    int i = 0;
    for (final Feature peak : row.getPeaks()) {
        // Only keep peak if it fulfills the filter criteria
        if (keepPeak[i]) {
            final Feature newPeak = new SimpleFeature(peak);
            PeakUtils.copyPeakProperties(peak, newPeak);
            newRow.addPeak(peak.getDataFile(), newPeak);
        }
        i++;
    }
    return newRow;
}

Example 72 with Feature

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

the class RowsFilterTask method filterPeakListRows.

/**
 * Filter the feature list rows.
 *
 * @param peakList feature list to filter.
 * @return a new feature list with rows of the original feature list that pass the filtering.
 */
private PeakList filterPeakListRows(final PeakList peakList) {
    // Create new feature list.
    final PeakList newPeakList = new SimplePeakList(peakList.getName() + ' ' + parameters.getParameter(RowsFilterParameters.SUFFIX).getValue(), peakList.getRawDataFiles());
    // Copy previous applied methods.
    for (final PeakListAppliedMethod method : peakList.getAppliedMethods()) {
        newPeakList.addDescriptionOfAppliedTask(method);
    }
    // Add task description to peakList.
    newPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(getTaskDescription(), parameters));
    // Get parameters.
    final boolean onlyIdentified = parameters.getParameter(RowsFilterParameters.HAS_IDENTITIES).getValue();
    final boolean filterByIdentityText = parameters.getParameter(RowsFilterParameters.IDENTITY_TEXT).getValue();
    final boolean filterByCommentText = parameters.getParameter(RowsFilterParameters.COMMENT_TEXT).getValue();
    final String groupingParameter = (String) parameters.getParameter(RowsFilterParameters.GROUPSPARAMETER).getValue();
    final boolean filterByMinPeakCount = parameters.getParameter(RowsFilterParameters.MIN_PEAK_COUNT).getValue();
    final boolean filterByMinIsotopePatternSize = parameters.getParameter(RowsFilterParameters.MIN_ISOTOPE_PATTERN_COUNT).getValue();
    final boolean filterByMzRange = parameters.getParameter(RowsFilterParameters.MZ_RANGE).getValue();
    final boolean filterByRtRange = parameters.getParameter(RowsFilterParameters.RT_RANGE).getValue();
    final boolean filterByDuration = parameters.getParameter(RowsFilterParameters.PEAK_DURATION).getValue();
    final boolean filterByFWHM = parameters.getParameter(RowsFilterParameters.FWHM).getValue();
    final boolean filterByCharge = parameters.getParameter(RowsFilterParameters.CHARGE).getValue();
    final boolean filterByKMD = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getValue();
    final boolean filterByMS2 = parameters.getParameter(RowsFilterParameters.MS2_Filter).getValue();
    final String removeRowString = parameters.getParameter(RowsFilterParameters.REMOVE_ROW).getValue();
    Double minCount = parameters.getParameter(RowsFilterParameters.MIN_PEAK_COUNT).getEmbeddedParameter().getValue();
    final boolean renumber = parameters.getParameter(RowsFilterParameters.Reset_ID).getValue();
    int rowsCount = 0;
    boolean removeRow = false;
    if (removeRowString.equals(RowsFilterParameters.removeRowChoices[0]))
        removeRow = false;
    else
        removeRow = true;
    // Keep rows that don't match any criteria. Keep by default.
    boolean filterRowCriteriaFailed = false;
    // Handle < 1 values for minPeakCount
    if ((minCount == null) || (minCount < 1))
        minCount = 1.0;
    // Round value down to nearest hole number
    int intMinCount = minCount.intValue();
    // Filter rows.
    final PeakListRow[] rows = peakList.getRows();
    totalRows = rows.length;
    for (processedRows = 0; !isCanceled() && processedRows < totalRows; processedRows++) {
        filterRowCriteriaFailed = false;
        final PeakListRow row = rows[processedRows];
        final int peakCount = getPeakCount(row, groupingParameter);
        // Check number of peaks.
        if (filterByMinPeakCount) {
            if (peakCount < intMinCount)
                filterRowCriteriaFailed = true;
        }
        // Check identities.
        if (onlyIdentified) {
            if (row.getPreferredPeakIdentity() == null)
                filterRowCriteriaFailed = true;
        }
        // Check average m/z.
        if (filterByMzRange) {
            final Range<Double> mzRange = parameters.getParameter(RowsFilterParameters.MZ_RANGE).getEmbeddedParameter().getValue();
            if (!mzRange.contains(row.getAverageMZ()))
                filterRowCriteriaFailed = true;
        }
        // Check average RT.
        if (filterByRtRange) {
            final Range<Double> rtRange = parameters.getParameter(RowsFilterParameters.RT_RANGE).getEmbeddedParameter().getValue();
            if (!rtRange.contains(row.getAverageRT()))
                filterRowCriteriaFailed = true;
        }
        // Search peak identity text.
        if (filterByIdentityText) {
            if (row.getPreferredPeakIdentity() == null)
                filterRowCriteriaFailed = true;
            if (row.getPreferredPeakIdentity() != null) {
                final String searchText = parameters.getParameter(RowsFilterParameters.IDENTITY_TEXT).getEmbeddedParameter().getValue().toLowerCase().trim();
                int numFailedIdentities = 0;
                PeakIdentity[] identities = row.getPeakIdentities();
                for (int index = 0; !isCanceled() && index < identities.length; index++) {
                    String rowText = identities[index].getName().toLowerCase().trim();
                    if (!rowText.contains(searchText))
                        numFailedIdentities += 1;
                }
                if (numFailedIdentities == identities.length)
                    filterRowCriteriaFailed = true;
            }
        }
        // Search peak comment text.
        if (filterByCommentText) {
            if (row.getComment() == null)
                filterRowCriteriaFailed = true;
            if (row.getComment() != null) {
                final String searchText = parameters.getParameter(RowsFilterParameters.COMMENT_TEXT).getEmbeddedParameter().getValue().toLowerCase().trim();
                final String rowText = row.getComment().toLowerCase().trim();
                if (!rowText.contains(searchText))
                    filterRowCriteriaFailed = true;
            }
        }
        // Calculate average duration and isotope pattern count.
        int maxIsotopePatternSizeOnRow = 1;
        double avgDuration = 0.0;
        final Feature[] peaks = row.getPeaks();
        for (final Feature p : peaks) {
            final IsotopePattern pattern = p.getIsotopePattern();
            if (pattern != null && maxIsotopePatternSizeOnRow < pattern.getNumberOfDataPoints()) {
                maxIsotopePatternSizeOnRow = pattern.getNumberOfDataPoints();
            }
            avgDuration += RangeUtils.rangeLength(p.getRawDataPointsRTRange());
        }
        // Check isotope pattern count.
        if (filterByMinIsotopePatternSize) {
            final int minIsotopePatternSize = parameters.getParameter(RowsFilterParameters.MIN_ISOTOPE_PATTERN_COUNT).getEmbeddedParameter().getValue();
            if (maxIsotopePatternSizeOnRow < minIsotopePatternSize)
                filterRowCriteriaFailed = true;
        }
        // Check average duration.
        avgDuration /= peakCount;
        if (filterByDuration) {
            final Range<Double> durationRange = parameters.getParameter(RowsFilterParameters.PEAK_DURATION).getEmbeddedParameter().getValue();
            if (!durationRange.contains(avgDuration))
                filterRowCriteriaFailed = true;
        }
        // Filter by FWHM range
        if (filterByFWHM) {
            final Range<Double> FWHMRange = parameters.getParameter(RowsFilterParameters.FWHM).getEmbeddedParameter().getValue();
            // If any of the peaks fail the FWHM criteria,
            Double FWHM_value = row.getBestPeak().getFWHM();
            if (FWHM_value != null && !FWHMRange.contains(FWHM_value))
                filterRowCriteriaFailed = true;
        }
        // Filter by charge range
        if (filterByCharge) {
            final Range<Integer> chargeRange = parameters.getParameter(RowsFilterParameters.CHARGE).getEmbeddedParameter().getValue();
            int charge = row.getBestPeak().getCharge();
            if (charge == 0 || !chargeRange.contains(charge))
                filterRowCriteriaFailed = true;
        }
        // Filter by KMD or RKM range
        if (filterByKMD) {
            // get embedded parameters
            final Range<Double> rangeKMD = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getEmbeddedParameters().getParameter(KendrickMassDefectFilterParameters.kendrickMassDefectRange).getValue();
            final String kendrickMassBase = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getEmbeddedParameters().getParameter(KendrickMassDefectFilterParameters.kendrickMassBase).getValue();
            final double shift = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getEmbeddedParameters().getParameter(KendrickMassDefectFilterParameters.shift).getValue();
            final int charge = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getEmbeddedParameters().getParameter(KendrickMassDefectFilterParameters.charge).getValue();
            final int divisor = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getEmbeddedParameters().getParameter(KendrickMassDefectFilterParameters.divisor).getValue();
            final boolean useRemainderOfKendrickMass = parameters.getParameter(RowsFilterParameters.KENDRICK_MASS_DEFECT).getEmbeddedParameters().getParameter(KendrickMassDefectFilterParameters.useRemainderOfKendrickMass).getValue();
            // get m/z
            Double valueMZ = row.getBestPeak().getMZ();
            // calc exact mass of Kendrick mass base
            double exactMassFormula = FormulaUtils.calculateExactMass(kendrickMassBase);
            // calc exact mass of Kendrick mass factor
            double kendrickMassFactor = Math.round(exactMassFormula / divisor) / (exactMassFormula / divisor);
            double defectOrRemainder = 0.0;
            if (!useRemainderOfKendrickMass) {
                // calc Kendrick mass defect
                defectOrRemainder = Math.ceil(charge * (valueMZ * kendrickMassFactor)) - charge * (valueMZ * kendrickMassFactor);
            } else {
                // calc Kendrick mass remainder
                defectOrRemainder = (charge * (divisor - Math.round(FormulaUtils.calculateExactMass(kendrickMassBase))) * valueMZ) / // 
                FormulaUtils.calculateExactMass(kendrickMassBase) - Math.floor((charge * (divisor - Math.round(FormulaUtils.calculateExactMass(kendrickMassBase))) * valueMZ) / FormulaUtils.calculateExactMass(kendrickMassBase));
            }
            // shift Kendrick mass defect or remainder of Kendrick mass
            double kendrickMassDefectShifted = defectOrRemainder + shift - Math.floor(defectOrRemainder + shift);
            // check if shifted Kendrick mass defect or remainder of Kendrick mass is in range
            if (!rangeKMD.contains(kendrickMassDefectShifted))
                filterRowCriteriaFailed = true;
        }
        // Check ms2 filter .
        if (filterByMS2) {
            // iterates the peaks
            int failCounts = 0;
            for (int i = 0; i < peakCount; i++) {
                if (row.getPeaks()[i].getMostIntenseFragmentScanNumber() < 1) {
                    failCounts++;
                // filterRowCriteriaFailed = true;
                // break;
                }
            }
            if (failCounts == peakCount) {
                filterRowCriteriaFailed = true;
            }
        }
        if (!filterRowCriteriaFailed && !removeRow) {
            // Only add the row if none of the criteria have failed.
            rowsCount++;
            PeakListRow resetRow = copyPeakRow(row);
            if (renumber) {
                resetRow.setID(rowsCount);
            }
            newPeakList.addRow(resetRow);
        }
        if (filterRowCriteriaFailed && removeRow) {
            // Only remove rows that match *all* of the criteria, so add
            // rows that fail any of the criteria.
            rowsCount++;
            PeakListRow resetRow = copyPeakRow(row);
            if (renumber) {
                resetRow.setID(rowsCount);
            }
            newPeakList.addRow(resetRow);
        }
    }
    return newPeakList;
}

Example 73 with Feature

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

the class RowsFilterTask method copyPeakRow.

/**
 * Create a copy of a feature list row.
 *
 * @param row the row to copy.
 * @return the newly created copy.
 */
private static PeakListRow copyPeakRow(final PeakListRow row) {
    // Copy the feature list row.
    final PeakListRow newRow = new SimplePeakListRow(row.getID());
    PeakUtils.copyPeakListRowProperties(row, newRow);
    // Copy the peaks.
    for (final Feature peak : row.getPeaks()) {
        final Feature newPeak = new SimpleFeature(peak);
        PeakUtils.copyPeakProperties(peak, newPeak);
        newRow.addPeak(peak.getDataFile(), newPeak);
    }
    // Add PeakInformation
    if (row.getPeakInformation() != null) {
        SimplePeakInformation information = new SimplePeakInformation(new HashMap<>(row.getPeakInformation().getAllProperties()));
        newRow.setPeakInformation(information);
    }
    return newRow;
}

Example 74 with Feature

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

the class PeakFinderTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running gap filler on " + peakList);
    // Calculate total number of scans in all files
    for (RawDataFile dataFile : peakList.getRawDataFiles()) {
        totalScans += dataFile.getNumOfScans(1);
    }
    processedScans = new AtomicInteger();
    // Create new feature list
    processedPeakList = new SimplePeakList(peakList + " " + suffix, peakList.getRawDataFiles());
    // Fill new feature list with empty rows
    for (int row = 0; row < peakList.getNumberOfRows(); row++) {
        PeakListRow sourceRow = peakList.getRow(row);
        PeakListRow newRow = new SimplePeakListRow(sourceRow.getID());
        newRow.setComment(sourceRow.getComment());
        for (PeakIdentity ident : sourceRow.getPeakIdentities()) {
            newRow.addPeakIdentity(ident, false);
        }
        if (sourceRow.getPreferredPeakIdentity() != null) {
            newRow.setPreferredPeakIdentity(sourceRow.getPreferredPeakIdentity());
        }
        processedPeakList.addRow(newRow);
    }
    if (rtCorrection) {
        totalScans *= 2;
        // Fill the gaps of a random sample using all the other samples and
        // take it as master list
        // to fill the gaps of the other samples
        masterSample = (int) Math.floor(Math.random() * peakList.getNumberOfRawDataFiles());
        fillList(MASTERLIST);
        // Process all raw data files
        fillList(!MASTERLIST);
    } else {
        // Process all raw data files
        IntStream rawStream = IntStream.range(0, peakList.getNumberOfRawDataFiles());
        if (useParallelStream)
            rawStream = rawStream.parallel();
        rawStream.forEach(i -> {
            // Canceled?
            if (isCanceled()) {
                // inside stream - only skips this element
                return;
            }
            RawDataFile dataFile = peakList.getRawDataFile(i);
            List<Gap> gaps = new ArrayList<Gap>();
            // if necessary
            for (int row = 0; row < peakList.getNumberOfRows(); row++) {
                // Canceled?
                if (isCanceled()) {
                    // inside stream - only skips this element
                    return;
                }
                PeakListRow sourceRow = peakList.getRow(row);
                PeakListRow newRow = processedPeakList.getRow(row);
                Feature sourcePeak = sourceRow.getPeak(dataFile);
                if (sourcePeak == null) {
                    // Create a new gap
                    Range<Double> mzRange = mzTolerance.getToleranceRange(sourceRow.getAverageMZ());
                    Range<Double> rtRange = rtTolerance.getToleranceRange(sourceRow.getAverageRT());
                    Gap newGap = new Gap(newRow, dataFile, mzRange, rtRange, intTolerance);
                    gaps.add(newGap);
                } else {
                    newRow.addPeak(dataFile, sourcePeak);
                }
            }
            // Stop processing this file if there are no gaps
            if (gaps.size() == 0) {
                processedScans.addAndGet(dataFile.getNumOfScans());
                return;
            }
            // Get all scans of this data file
            int[] scanNumbers = dataFile.getScanNumbers(1);
            // Process each scan
            for (int scanNumber : scanNumbers) {
                // Canceled?
                if (isCanceled()) {
                    // inside stream - only skips this element
                    return;
                }
                // Get the scan
                Scan scan = dataFile.getScan(scanNumber);
                // Feed this scan to all gaps
                for (Gap gap : gaps) {
                    gap.offerNextScan(scan);
                }
                processedScans.incrementAndGet();
            }
            // Finalize gaps
            for (Gap gap : gaps) {
                gap.noMoreOffers();
            }
        });
    }
    // terminate - stream only skips all elements
    if (isCanceled())
        return;
    // Append processed feature list to the project
    project.addPeakList(processedPeakList);
    // Add quality parameters to peaks
    QualityParameters.calculateQualityParameters(processedPeakList);
    // Add task description to peakList
    processedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Gap filling ", parameters));
    // Remove the original peaklist if requested
    if (removeOriginal)
        project.removePeakList(peakList);
    logger.info("Finished gap-filling on " + peakList);
    setStatus(TaskStatus.FINISHED);
}

Example 75 with Feature

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

the class MultiThreadPeakFinderTask method run.

public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running multithreaded gap filler " + taskIndex + " on raw files " + (start + 1) + "-" + endexcl + " of pkl:" + peakList);
    // Calculate total number of scans in all files
    for (int i = start; i < endexcl; i++) {
        RawDataFile dataFile = peakList.getRawDataFile(i);
        totalScans += dataFile.getNumOfScans(1);
    }
    // Process all raw data files
    for (int i = start; i < endexcl; i++) {
        RawDataFile dataFile = peakList.getRawDataFile(i);
        // Canceled?
        if (isCanceled()) {
            return;
        }
        List<Gap> gaps = new ArrayList<Gap>();
        // if necessary
        for (int row = 0; row < peakList.getNumberOfRows(); row++) {
            PeakListRow sourceRow = peakList.getRow(row);
            PeakListRow newRow = processedPeakList.getRow(row);
            Feature sourcePeak = sourceRow.getPeak(dataFile);
            if (sourcePeak == null) {
                // Create a new gap
                Range<Double> mzRange = mzTolerance.getToleranceRange(sourceRow.getAverageMZ());
                Range<Double> rtRange = rtTolerance.getToleranceRange(sourceRow.getAverageRT());
                Gap newGap = new Gap(newRow, dataFile, mzRange, rtRange, intTolerance);
                gaps.add(newGap);
            } else {
                newRow.addPeak(dataFile, sourcePeak);
            }
        }
        // Stop processing this file if there are no gaps
        if (gaps.isEmpty()) {
            processedScans += dataFile.getNumOfScans();
            continue;
        }
        // Get all scans of this data file
        int[] scanNumbers = dataFile.getScanNumbers(1);
        // Process each scan
        for (int scanNumber : scanNumbers) {
            // Canceled?
            if (isCanceled()) {
                return;
            }
            // Get the scan
            Scan scan = dataFile.getScan(scanNumber);
            // Feed this scan to all gaps
            for (Gap gap : gaps) {
                gap.offerNextScan(scan);
            }
            processedScans++;
        }
        // Finalize gaps
        for (Gap gap : gaps) {
            gap.noMoreOffers();
        }
    }
    // first notify listener
    listener.accept(processedPeakList);
    logger.info("Finished sub task: Multithreaded gap filler " + taskIndex + " on raw files " + (start + 1) + "-" + endexcl + " of pkl:" + peakList);
    setStatus(TaskStatus.FINISHED);
}