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

Example 21 with SimpleFeature

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

the class PeakUtils method copyPeakRow.

/**
 * Creates a copy of a PeakListRow.
 * @param row A row.
 * @return A copy of row.
 */
public 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);
    }
    return newRow;
}

Example 22 with SimpleFeature

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

the class ADAPInterface method peakToFeature.

@Nonnull
public static Feature peakToFeature(@Nonnull RawDataFile file, @Nonnull BetterPeak peak) {
    Chromatogram chromatogram = peak.chromatogram;
    // Retrieve scan numbers
    int representativeScan = 0;
    int[] scanNumbers = new int[chromatogram.length];
    int count = 0;
    for (int num : file.getScanNumbers()) {
        double retTime = file.getScan(num).getRetentionTime();
        Double intensity = chromatogram.getIntensity(retTime, false);
        if (intensity != null)
            scanNumbers[count++] = num;
        if (retTime == peak.getRetTime())
            representativeScan = num;
    }
    // Calculate peak area
    double area = 0.0;
    for (int i = 1; i < chromatogram.length; ++i) {
        double base = (chromatogram.xs[i] - chromatogram.xs[i - 1]) * 60d;
        double height = 0.5 * (chromatogram.ys[i] + chromatogram.ys[i - 1]);
        area += base * height;
    }
    // Create array of DataPoints
    DataPoint[] dataPoints = new DataPoint[chromatogram.length];
    count = 0;
    for (double intensity : chromatogram.ys) dataPoints[count++] = new SimpleDataPoint(peak.getMZ(), intensity);
    return new SimpleFeature(file, peak.getMZ(), peak.getRetTime(), peak.getIntensity(), area, scanNumbers, dataPoints, Feature.FeatureStatus.ESTIMATED, representativeScan, representativeScan, new int[] {}, Range.closed(peak.getFirstRetTime(), peak.getLastRetTime()), Range.closed(peak.getMZ() - 0.01, peak.getMZ() + 0.01), Range.closed(0.0, peak.getIntensity()));
}

Example 23 with SimpleFeature

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

the class MzTabImportTask method importSmallMolecules.

private void importSmallMolecules(PeakList newPeakList, MZTabFile mzTabFile, Map<Integer, RawDataFile> rawDataFiles) {
    SortedMap<Integer, Assay> assayMap = mzTabFile.getMetadata().getAssayMap();
    Collection<SmallMolecule> smallMolecules = mzTabFile.getSmallMolecules();
    // Loop through SML data
    String formula, description, database, url = "";
    double mzExp = 0, abundance = 0, peak_mz = 0, peak_rt = 0, peak_height = 0, rtValue = 0;
    // int charge = 0;
    int rowCounter = 0;
    for (SmallMolecule smallMolecule : smallMolecules) {
        // Stop the process if cancel() was called
        if (isCanceled())
            return;
        rowCounter++;
        formula = smallMolecule.getChemicalFormula();
        // smile = smallMolecule.getSmiles();
        // inchiKey = smallMolecule.getInchiKey();
        description = smallMolecule.getDescription();
        // species = smallMolecule.getSpecies();
        database = smallMolecule.getDatabase();
        if (smallMolecule.getURI() != null) {
            url = smallMolecule.getURI().toString();
        }
        String identifier = smallMolecule.getIdentifier().toString();
        SplitList<Double> rt = smallMolecule.getRetentionTime();
        if (smallMolecule.getExpMassToCharge() != null) {
            mzExp = smallMolecule.getExpMassToCharge();
        }
        // Calculate average RT if multiple values are available
        if (rt != null && !rt.isEmpty()) {
            rtValue = DoubleMath.mean(rt);
        }
        if ((url != null) && (url.equals("null"))) {
            url = null;
        }
        if (identifier.equals("null")) {
            identifier = null;
        }
        if (description == null && identifier != null) {
            description = identifier;
        }
        // Add shared information to row
        SimplePeakListRow newRow = new SimplePeakListRow(rowCounter);
        newRow.setAverageMZ(mzExp);
        newRow.setAverageRT(rtValue);
        if (description != null) {
            SimplePeakIdentity newIdentity = new SimplePeakIdentity(description, formula, database, identifier, url);
            newRow.addPeakIdentity(newIdentity, false);
        }
        // Add raw data file entries to row
        for (Entry<Integer, RawDataFile> rawDataEntry : rawDataFiles.entrySet()) {
            RawDataFile rawData = rawDataEntry.getValue();
            Assay dataFileAssay = assayMap.get(rawDataEntry.getKey());
            abundance = 0;
            peak_mz = 0;
            peak_rt = 0;
            peak_height = 0;
            if (smallMolecule.getAbundanceColumnValue(dataFileAssay) != null) {
                abundance = smallMolecule.getAbundanceColumnValue(dataFileAssay);
            }
            if (smallMolecule.getOptionColumnValue(dataFileAssay, "peak_mz") != null) {
                peak_mz = Double.parseDouble(smallMolecule.getOptionColumnValue(dataFileAssay, "peak_mz"));
            } else {
                peak_mz = mzExp;
            }
            if (smallMolecule.getOptionColumnValue(dataFileAssay, "peak_rt") != null) {
                peak_rt = Double.parseDouble(smallMolecule.getOptionColumnValue(dataFileAssay, "peak_rt"));
            } else {
                peak_rt = rtValue;
            }
            if (smallMolecule.getOptionColumnValue(dataFileAssay, "peak_height") != null) {
                peak_height = Double.parseDouble(smallMolecule.getOptionColumnValue(dataFileAssay, "peak_height"));
            } else {
                peak_height = 0.0;
            }
            int[] scanNumbers = {};
            DataPoint[] finalDataPoint = new DataPoint[1];
            finalDataPoint[0] = new SimpleDataPoint(peak_mz, peak_height);
            int representativeScan = 0;
            int fragmentScan = 0;
            int[] allFragmentScans = new int[] { 0 };
            Range<Double> finalRTRange = Range.singleton(peak_rt);
            Range<Double> finalMZRange = Range.singleton(peak_mz);
            Range<Double> finalIntensityRange = Range.singleton(peak_height);
            FeatureStatus status = FeatureStatus.DETECTED;
            Feature peak = new SimpleFeature(rawData, peak_mz, peak_rt, peak_height, abundance, scanNumbers, finalDataPoint, status, representativeScan, fragmentScan, allFragmentScans, finalRTRange, finalMZRange, finalIntensityRange);
            if (abundance > 0) {
                newRow.addPeak(rawData, peak);
            }
        }
        // Add row to feature list
        newPeakList.addRow(newRow);
    }
}

Example 24 with SimpleFeature

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

the class PeakListOpenHandler_2_5 method endElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
 *      java.lang.String)
 */
@Override
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // <NAME>
    if (qName.equals(PeakListElementName_2_5.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading feature list: " + name);
        peakListName = name;
    }
    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_5.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }
    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_5.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }
    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_5.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException("Cannot open feature list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }
    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_5.SCAN_ID.getElementName())) {
        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        scanNumbers = new int[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                scanNumbers[i] = dataInputStream.readInt();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }
    // <REPRESENTATIVE_SCAN>
    if (qName.equals(PeakListElementName_2_5.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }
    // <FRAGMENT_SCAN>
    if (qName.equals(PeakListElementName_2_5.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }
    // <All_MS2_FRAGMENT_SCANS>
    if (qName.equals(PeakListElementName_2_5.ALL_MS2_FRAGMENT_SCANS.getElementName())) {
        Integer fragmentNumber = Integer.valueOf(getTextOfElement());
        currentAllMS2FragmentScans.add(fragmentNumber);
    }
    // <MASS>
    if (qName.equals(PeakListElementName_2_5.MZ.getElementName())) {
        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        masses = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                masses[i] = dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }
    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_5.HEIGHT.getElementName())) {
        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        intensities = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                intensities[i] = dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }
    // <PEAK>
    if (qName.equals(PeakListElementName_2_5.PEAK.getElementName())) {
        DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
        Range<Double> peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
        RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);
        if (dataFile == null)
            throw new SAXException("Error in project: data file " + peakColumnID + " not found");
        for (int i = 0; i < numOfMZpeaks; i++) {
            Scan sc = dataFile.getScan(scanNumbers[i]);
            double retentionTime = sc.getRetentionTime();
            double mz = masses[i];
            double intensity = intensities[i];
            if (peakIntensityRange == null) {
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            if (intensity > 0) {
                if (peakRTRange == null) {
                    peakRTRange = Range.singleton(retentionTime);
                } else {
                    peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                }
            }
            if (mz > 0.0) {
                mzPeaks[i] = new SimpleDataPoint(mz, intensity);
                if (peakMZRange == null)
                    peakMZRange = Range.singleton(mz);
                else
                    peakMZRange = peakMZRange.span(Range.singleton(mz));
            }
        }
        FeatureStatus status = FeatureStatus.valueOf(peakStatus);
        // convert vector of allMS2FragmentScans to array
        allMS2FragmentScanNumbers = new int[currentAllMS2FragmentScans.size()];
        for (int i = 0; i < allMS2FragmentScanNumbers.length; i++) {
            allMS2FragmentScanNumbers[i] = currentAllMS2FragmentScans.get(i);
        }
        // clear all MS2 fragment scan numbers list for next peak
        currentAllMS2FragmentScans.clear();
        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status, representativeScan, fragmentScan, allMS2FragmentScanNumbers, peakRTRange, peakMZRange, peakIntensityRange);
        peak.setCharge(currentPeakCharge);
        if (currentIsotopes.size() > 0) {
            SimpleIsotopePattern newPattern = new SimpleIsotopePattern(currentIsotopes.toArray(new DataPoint[0]), currentIsotopePatternStatus, currentIsotopePatternDescription);
            peak.setIsotopePattern(newPattern);
            currentIsotopes.clear();
        }
        peak.setParentChromatogramRowID(parentChromatogramRowID);
        buildingRow.addPeak(dataFile, peak);
    }
    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_5.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }
    // <INFO_PROPERTY>
    if (qName.equals(PeakListElementName_2_5.INFO_PROPERTY.getElementName())) {
        informationProperties.put(infoPropertyName, getTextOfElement());
    }
    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_5.PEAK_IDENTITY.getElementName())) {
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }
    if (qName.equals(PeakListElementName_2_5.PEAK_INFORMATION.getElementName())) {
        PeakInformation information = new SimplePeakInformation(informationProperties);
        buildingRow.setPeakInformation(information);
    }
    // <ROW>
    if (qName.equals(PeakListElementName_2_5.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }
    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_5.ISOTOPE.getElementName())) {
        String text = getTextOfElement();
        String[] items = text.split(":");
        double mz = Double.valueOf(items[0]);
        double intensity = Double.valueOf(items[1]);
        DataPoint isotope = new SimpleDataPoint(mz, intensity);
        currentIsotopes.add(isotope);
    }
    if (qName.equals(PeakListElementName_2_5.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }
    if (qName.equals(PeakListElementName_2_5.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }
}

Example 25 with SimpleFeature

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

the class SmoothingTask method run.

@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    try {
        // Get filter weights.
        final double[] filterWeights = SavitzkyGolayFilter.getNormalizedWeights(filterWidth);
        // Create new feature list
        newPeakList = new SimplePeakList(origPeakList + " " + suffix, origPeakList.getRawDataFiles());
        // Process each row.
        for (final PeakListRow row : origPeakList.getRows()) {
            if (!isCanceled()) {
                // Create a new peak-list row.
                final int originalID = row.getID();
                final PeakListRow newRow = new SimplePeakListRow(originalID);
                // Process each peak.
                for (final Feature peak : row.getPeaks()) {
                    if (!isCanceled()) {
                        // Copy original peak intensities.
                        final int[] scanNumbers = peak.getScanNumbers();
                        final int numScans = scanNumbers.length;
                        final double[] intensities = new double[numScans];
                        for (int i = 0; i < numScans; i++) {
                            final DataPoint dataPoint = peak.getDataPoint(scanNumbers[i]);
                            intensities[i] = dataPoint == null ? 0.0 : dataPoint.getIntensity();
                        }
                        // Smooth peak.
                        final double[] smoothed = convolve(intensities, filterWeights);
                        // Measure peak (max, ranges, area etc.)
                        final RawDataFile dataFile = peak.getDataFile();
                        final DataPoint[] newDataPoints = new DataPoint[numScans];
                        double maxIntensity = 0.0;
                        int maxScanNumber = -1;
                        DataPoint maxDataPoint = null;
                        Range<Double> intensityRange = null;
                        double area = 0.0;
                        for (int i = 0; i < numScans; i++) {
                            final int scanNumber = scanNumbers[i];
                            final DataPoint dataPoint = peak.getDataPoint(scanNumber);
                            final double intensity = smoothed[i];
                            if (dataPoint != null && intensity > 0.0) {
                                // Create a new data point.
                                final double mz = dataPoint.getMZ();
                                final double rt = dataFile.getScan(scanNumber).getRetentionTime();
                                final DataPoint newDataPoint = new SimpleDataPoint(mz, intensity);
                                newDataPoints[i] = newDataPoint;
                                // Track maximum intensity data point.
                                if (intensity > maxIntensity) {
                                    maxIntensity = intensity;
                                    maxScanNumber = scanNumber;
                                    maxDataPoint = newDataPoint;
                                }
                                // Update ranges.
                                if (intensityRange == null) {
                                    intensityRange = Range.singleton(intensity);
                                } else {
                                    intensityRange = intensityRange.span(Range.singleton(intensity));
                                }
                                // Accumulate peak area.
                                if (i != 0) {
                                    final DataPoint lastDP = newDataPoints[i - 1];
                                    final double lastIntensity = lastDP == null ? 0.0 : lastDP.getIntensity();
                                    final double lastRT = dataFile.getScan(scanNumbers[i - 1]).getRetentionTime();
                                    area += (rt - lastRT) * 60d * (intensity + lastIntensity) / 2.0;
                                }
                            }
                        }
                        assert maxDataPoint != null;
                        if (!isCanceled() && maxScanNumber >= 0) {
                            // Create a new peak.
                            newRow.addPeak(dataFile, new SimpleFeature(dataFile, maxDataPoint.getMZ(), peak.getRT(), maxIntensity, area, scanNumbers, newDataPoints, peak.getFeatureStatus(), maxScanNumber, peak.getMostIntenseFragmentScanNumber(), peak.getAllMS2FragmentScanNumbers(), peak.getRawDataPointsRTRange(), peak.getRawDataPointsMZRange(), intensityRange));
                        }
                    }
                }
                newPeakList.addRow(newRow);
                progress++;
            }
        }
        // Finish up.
        if (!isCanceled()) {
            // Add new peak-list to the project.
            project.addPeakList(newPeakList);
            // Add quality parameters to peaks
            QualityParameters.calculateQualityParameters(newPeakList);
            // Remove the original peak-list if requested.
            if (removeOriginal) {
                project.removePeakList(origPeakList);
            }
            // Copy previously applied methods
            for (final PeakListAppliedMethod method : origPeakList.getAppliedMethods()) {
                newPeakList.addDescriptionOfAppliedTask(method);
            }
            // Add task description to peak-list.
            newPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Peaks smoothed by Savitzky-Golay filter", parameters));
            LOG.finest("Finished peak smoothing: " + progress + " rows processed");
            setStatus(TaskStatus.FINISHED);
        }
    } catch (Throwable t) {
        LOG.log(Level.SEVERE, "Smoothing error", t);
        setErrorMessage(t.getMessage());
        setStatus(TaskStatus.ERROR);
    }
}