Example usage for com.google.common.collect Range singleton

List of usage examples for com.google.common.collect Range singleton

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Introduction

In this page you can find the example usage for com.google.common.collect Range singleton.

Prototype

public static <C extends Comparable<?>> Range<C> singleton(C value)

Source Link

Document

Returns a range that Range#contains(Comparable) contains only the given value.

Usage

From source file:net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchTask.java

/**
 * Perform CAMERA search./*www .jav  a2  s .  co  m*/
 *
 * @param rawFile
 *            raw data file of peak list to process.
 */
private void cameraSearch(final RawDataFile rawFile) {

    LOG.finest("Detecting peaks.");

    errorMsg = null;
    try {

        String[] reqPackages = { "CAMERA" };
        String[] reqPackagesVersions = { CAMERA_VERSION };
        this.rSession = new RSessionWrapper("Camera search feature", reqPackages, reqPackagesVersions);
        this.rSession.open();

        // Create empty peaks matrix.
        this.rSession.eval(
                "columnHeadings <- c('mz','mzmin','mzmax','rt','rtmin','rtmax','into','intb','maxo','sn')");
        this.rSession.eval("peaks <- matrix(nrow=0, ncol=length(columnHeadings))");
        this.rSession.eval("colnames(peaks) <- columnHeadings");

        // Initialize.
        final Feature[] peaks = peakList.getPeaks(rawFile);
        progress = 0.0;

        // Initialize scan map.
        final Map<Scan, Set<DataPoint>> peakDataPointsByScan = new HashMap<Scan, Set<DataPoint>>(
                rawFile.getNumOfScans(MS_LEVEL));
        int dataPointCount = 0;
        for (final int scanNumber : rawFile.getScanNumbers(MS_LEVEL)) {

            // Create a set to hold data points (sorted by m/z).
            final Set<DataPoint> dataPoints = new TreeSet<DataPoint>(ASCENDING_MASS_SORTER);

            // Add a dummy data point.
            dataPoints.add(new SimpleDataPoint(0.0, 0.0));
            dataPointCount++;

            // Map the set.
            peakDataPointsByScan.put(rawFile.getScan(scanNumber), dataPoints);
        }

        // Add peaks.
        // 80 percents for building peaks list.
        double progressInc = 0.8 / (double) peaks.length;
        for (final Feature peak : peaks) {

            // Get peak data.
            Range<Double> rtRange = null;
            Range<Double> intRange = null;
            final double mz = peak.getMZ();

            // Get the peak's data points per scan.
            for (final int scanNumber : peak.getScanNumbers()) {

                final Scan scan = rawFile.getScan(scanNumber);
                if (scan.getMSLevel() != MS_LEVEL) {

                    throw new IllegalStateException(
                            "CAMERA can only process peak lists from MS-level " + MS_LEVEL);
                }

                // Copy the data point.
                final DataPoint dataPoint = peak.getDataPoint(scanNumber);
                if (dataPoint != null) {

                    final double intensity = dataPoint.getIntensity();
                    peakDataPointsByScan.get(scan).add(new SimpleDataPoint(mz, intensity));
                    dataPointCount++;

                    // Update RT & intensity range.
                    final double rt = scan.getRetentionTime();
                    if (rtRange == null) {
                        rtRange = Range.singleton(rt);
                        intRange = Range.singleton(intensity);
                    } else {
                        rtRange = rtRange.span(Range.singleton(rt));
                        intRange = intRange.span(Range.singleton(intensity));
                    }

                }
            }

            // Set peak values.
            final double area = peak.getArea();
            final double maxo = intRange == null ? peak.getHeight() : intRange.upperEndpoint();
            final double rtMin = (rtRange == null ? peak.getRawDataPointsRTRange() : rtRange).lowerEndpoint();
            final double rtMax = (rtRange == null ? peak.getRawDataPointsRTRange() : rtRange).upperEndpoint();

            // Add peak row.
            this.rSession.eval("peaks <- rbind(peaks, c(" + mz + ", " // mz
                    + mz + ", " // mzmin: use the same as mz.
                    + mz + ", " // mzmax: use the same as mz.
                    + peak.getRT() + ", " // rt
                    + rtMin + ", " // rtmin
                    + rtMax + ", " // rtmax
                    + area + ", " // into: peak area.
                    + area + ", " // intb: doesn't affect result, use area.
                    + maxo + ", " // maxo
                    + SIGNAL_TO_NOISE + "))", false);

            progress += progressInc;
        }

        // 20 percents (5*4) for building pseudo-isotopes groups.
        progressInc = 0.05;

        // Create R vectors.
        final int scanCount = peakDataPointsByScan.size();
        final double[] scanTimes = new double[scanCount];
        final int[] scanIndices = new int[scanCount];
        final double[] masses = new double[dataPointCount];
        final double[] intensities = new double[dataPointCount];

        // Fill vectors.
        int scanIndex = 0;
        int pointIndex = 0;
        for (final int scanNumber : rawFile.getScanNumbers(MS_LEVEL)) {

            final Scan scan = rawFile.getScan(scanNumber);
            scanTimes[scanIndex] = scan.getRetentionTime();
            scanIndices[scanIndex] = pointIndex + 1;
            scanIndex++;

            for (final DataPoint dataPoint : peakDataPointsByScan.get(scan)) {

                masses[pointIndex] = dataPoint.getMZ();
                intensities[pointIndex] = dataPoint.getIntensity();
                pointIndex++;
            }
        }

        // Set vectors.
        this.rSession.assign("scantime", scanTimes);
        this.rSession.assign("scanindex", scanIndices);
        this.rSession.assign("mass", masses);
        this.rSession.assign("intensity", intensities);

        // Construct xcmsRaw object
        this.rSession.eval("xRaw <- new(\"xcmsRaw\")");
        this.rSession.eval("xRaw@tic <- intensity");
        this.rSession.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE);
        this.rSession.eval("xRaw@scanindex <- scanindex");
        this.rSession.eval("xRaw@env$mz <- mass");
        this.rSession.eval("xRaw@env$intensity <- intensity");

        // Create the xcmsSet object.
        this.rSession.eval("xs <- new(\"xcmsSet\")");

        // Set peaks.
        this.rSession.eval("xs@peaks <- peaks");

        // Set file (dummy) file path.
        this.rSession.eval("xs@filepaths  <- ''");

        // Set sample name.
        this.rSession.assign("sampleName", peakList.getName());
        this.rSession.eval("sampnames(xs) <- sampleName");

        // Create an empty xsAnnotate.
        this.rSession.eval("an <- xsAnnotate(xs, sample=1)");

        // Group by RT.
        this.rSession.eval("an <- groupFWHM(an, sigma=" + fwhmSigma + ", perfwhm=" + fwhmPercentage + ')');
        progress += progressInc;

        // Identify isotopes.
        this.rSession.eval("an <- findIsotopes(an, maxcharge=" + isoMaxCharge + ", maxiso=" + isoMaxCount
                + ", ppm=" + isoMassTolerance.getPpmTolerance() + ", mzabs=" + isoMassTolerance.getMzTolerance()
                + ')');
        progress += progressInc;

        // Split groups by correlating peak shape (need to set xraw to raw
        // data).
        this.rSession.eval("an <- groupCorr(an, calcIso=TRUE, xraw=xRaw, cor_eic_th=" + corrThreshold
                + ", pval=" + corrPValue + ')');
        progress += progressInc;

        // Get the peak list.
        this.rSession.eval("peakList <- getPeaklist(an)");

        // Extract the pseudo-spectra and isotope annotations from the peak
        // list.
        rSession.eval("pcgroup <- as.integer(peakList$pcgroup)");
        rSession.eval("isotopes <- peakList$isotopes");
        final int[] spectra = (int[]) rSession.collect("pcgroup");
        final String[] isotopes = (String[]) rSession.collect("isotopes");

        // Add identities.
        if (spectra != null) {

            addPseudoSpectraIdentities(peaks, spectra, isotopes);
        }
        progress += progressInc;
        // Turn off R instance, once task ended gracefully.
        if (!this.userCanceled)
            this.rSession.close(false);

    } catch (RSessionWrapperException e) {
        if (!this.userCanceled) {
            errorMsg = "'R computing error' during CAMERA search. \n" + e.getMessage();
            e.printStackTrace();
        }
    } catch (Exception e) {
        if (!this.userCanceled) {
            errorMsg = "'Unknown error' during CAMERA search. \n" + e.getMessage();
            e.printStackTrace();
        }
    }

    // Turn off R instance, once task ended UNgracefully.
    try {
        if (!this.userCanceled)
            this.rSession.close(this.userCanceled);
    } catch (RSessionWrapperException e) {
        if (!this.userCanceled) {
            // Do not override potential previous error message.
            if (errorMsg == null) {
                errorMsg = e.getMessage();
            }
        } else {
            // User canceled: Silent.
        }
    }

    // Report error.
    if (errorMsg != null) {
        setErrorMessage(errorMsg);
        setStatus(TaskStatus.ERROR);
    }
}

From source file:com.google.eclipse.protobuf.validation.ProtobufJavaValidator.java

@Check
public void checkForIndexConflicts(Message message) {
    Multimap<EObject, Range<Long>> rangeUsages = LinkedHashMultimap.create();

    for (Reserved reserved : getOwnedElements(message, Reserved.class)) {
        for (IndexRange indexRange : Iterables.filter(reserved.getReservations(), IndexRange.class)) {
            try {
                Range<Long> range = indexRanges.toLongRange(indexRange);
                errorOnConflicts(range, rangeUsages, indexRange, null);
                rangeUsages.put(reserved, range);
            } catch (BackwardsRangeException e) {
                // Do not try to find conflicts with invalid ranges.
            }//  w  w  w .j a  v  a  2s  . c  o m
        }
    }

    for (Extensions extensions : getOwnedElements(message, Extensions.class)) {
        for (IndexRange indexRange : extensions.getRanges()) {
            try {
                Range<Long> range = indexRanges.toLongRange(indexRange);
                errorOnConflicts(range, rangeUsages, indexRange, null);
                rangeUsages.put(extensions, range);
            } catch (BackwardsRangeException e) {
                // Do not try to find conflicts with invalid ranges.
            }
        }
    }

    for (IndexedElement element : getOwnedElements(message, IndexedElement.class)) {
        long index = indexedElements.indexOf(element);
        Range<Long> range = Range.singleton(index);
        EStructuralFeature feature = indexedElements.indexFeatureOf(element);
        errorOnConflicts(range, rangeUsages, element, feature);
        rangeUsages.put(element, range);
    }
}

From source file:io.github.msdk.io.nativeformats.RawDumpParser.java

@SuppressWarnings("null")
private void parseLine(String line, InputStream dumpStream) throws MSDKException, IOException {

    if (line.startsWith("ERROR: ")) {
        throw (new MSDKException(line));
    }// w w  w .ja v  a 2  s .  c om

    if (line.startsWith("NUMBER OF SCANS: ")) {
        totalScans = Integer.parseInt(line.substring("NUMBER OF SCANS: ".length()));
    }

    if (line.startsWith("SCAN NUMBER: ")) {
        scanNumber = Integer.parseInt(line.substring("SCAN NUMBER: ".length()));
    }

    if (line.startsWith("SCAN ID: ")) {
        scanId = line.substring("SCAN ID: ".length());
    }

    if (line.startsWith("MS LEVEL: ")) {
        msLevel = Integer.parseInt(line.substring("MS LEVEL: ".length()));
    }

    if (line.startsWith("POLARITY: ")) {
        if (line.contains("-"))
            polarity = PolarityType.NEGATIVE;
        else if (line.contains("+"))
            polarity = PolarityType.POSITIVE;
        else
            polarity = PolarityType.UNKNOWN;

        // For Thermo RAW files, the polarity is sometimes not recognized.
        // In such case, we can parse it from the scan filter line (scanId).
        if ((polarity == PolarityType.UNKNOWN) && (newRawFile.getRawDataFileType() == FileType.THERMO_RAW)
                && (!Strings.isNullOrEmpty(scanId))) {
            if (scanId.startsWith("-"))
                polarity = PolarityType.NEGATIVE;
            else if (scanId.startsWith("+"))
                polarity = PolarityType.POSITIVE;
        }

    }

    if (line.startsWith("RETENTION TIME: ")) {
        // Retention time is reported in minutes.
        retentionTime = Float.parseFloat(line.substring("RETENTION TIME: ".length())) * 60.0f;
    }

    if (line.startsWith("PRECURSOR: ")) {
        String tokens[] = line.split(" ");
        double token2 = Double.parseDouble(tokens[1]);
        int token3 = Integer.parseInt(tokens[2]);

        precursorMz = token2;
        precursorCharge = token3;

        // For Thermo RAW files, the MSFileReader library sometimes
        // returns 0.0 for precursor m/z. In such case, we can parse
        // the precursor m/z from the scan filter line (scanId).
        // Examples:
        // + c ESI SRM ms2 165.000 [118.600-119.600]
        // FTMS + p ESI d Full ms2 279.16@hcd25.00 [50.00-305.00]
        if ((precursorMz == 0.0) && (newRawFile.getRawDataFileType() == FileType.THERMO_RAW)
                && (!Strings.isNullOrEmpty(scanId))) {
            Pattern precursorPattern = Pattern.compile(".* ms\\d+ (\\d+\\.\\d+)[@ ]");
            Matcher m = precursorPattern.matcher(scanId);
            if (m.find()) {
                String precursorMzString = m.group(1);
                try {
                    precursorMz = Double.parseDouble(precursorMzString);
                } catch (Exception e) {
                    e.printStackTrace();
                    // ignore
                }
            }
        }

    }

    if (line.startsWith("MASS VALUES: ")) {
        Pattern p = Pattern.compile("MASS VALUES: (\\d+) x (\\d+) BYTES");
        Matcher m = p.matcher(line);
        if (!m.matches())
            throw new MSDKException("Could not parse line " + line);
        numOfDataPoints = Integer.parseInt(m.group(1));

        // Allocate space
        if (mzValues.length < numOfDataPoints)
            mzValues = new double[numOfDataPoints * 2];
        if (intensityValues.length < numOfDataPoints)
            intensityValues = new float[numOfDataPoints * 2];

        final int byteSize = Integer.parseInt(m.group(2));

        final int numOfBytes = numOfDataPoints * byteSize;
        if (byteBuffer.length < numOfBytes)
            byteBuffer = new byte[numOfBytes * 2];
        dumpStream.read(byteBuffer, 0, numOfBytes);

        ByteBuffer mzByteBuffer = ByteBuffer.wrap(byteBuffer, 0, numOfBytes).order(ByteOrder.LITTLE_ENDIAN);

        for (int i = 0; i < numOfDataPoints; i++) {
            if (byteSize == 8)
                mzValues[i] = mzByteBuffer.getDouble();
            else
                mzValues[i] = mzByteBuffer.getFloat();
        }

    }

    if (line.startsWith("INTENSITY VALUES: ")) {
        Pattern p = Pattern.compile("INTENSITY VALUES: (\\d+) x (\\d+) BYTES");
        Matcher m = p.matcher(line);
        if (!m.matches())
            throw new MSDKException("Could not parse line " + line);
        // numOfDataPoints must be same for MASS VALUES and INTENSITY
        // VALUES
        if (numOfDataPoints != Integer.parseInt(m.group(1))) {
            throw new MSDKException("Scan " + scanNumber + " contained " + numOfDataPoints
                    + " mass values, but " + m.group(1) + " intensity values");
        }
        final int byteSize = Integer.parseInt(m.group(2));

        final int numOfBytes = numOfDataPoints * byteSize;
        if (byteBuffer.length < numOfBytes)
            byteBuffer = new byte[numOfBytes * 2];
        dumpStream.read(byteBuffer, 0, numOfBytes);

        ByteBuffer intensityByteBuffer = ByteBuffer.wrap(byteBuffer, 0, numOfBytes)
                .order(ByteOrder.LITTLE_ENDIAN);

        for (int i = 0; i < numOfDataPoints; i++) {
            if (byteSize == 8)
                intensityValues[i] = (float) intensityByteBuffer.getDouble();
            else
                intensityValues[i] = intensityByteBuffer.getFloat();
        }
    }

    if (line.startsWith("END OF SCAN")) {

        // Auto-detect whether this scan is centroided
        MsSpectrumType spectrumType = SpectrumTypeDetectionAlgorithm.detectSpectrumType(mzValues,
                intensityValues, numOfDataPoints);

        // Create a new MS function
        MsFunction msFunction = null;
        if ((newRawFile.getRawDataFileType() == FileType.THERMO_RAW) && (!Strings.isNullOrEmpty(scanId))) {
            // Parse the MS function from the scan filter line, e.g.
            // + c SRM ms2 469.40@cid23.00 [423.30-425.30]
            // + p ESI Q1MS [181.653-182.582, 507.779-508.708]

            String scanIdLowerCase = scanId.toLowerCase();

            for (String fn : thermoMsFunctions) {
                if (scanIdLowerCase.contains(fn)) {
                    msFunction = MSDKObjectBuilder.getMsFunction(fn, msLevel);
                    break;
                }
            }

        }
        if (msFunction == null)
            msFunction = MSDKObjectBuilder.getMsFunction(msLevel);

        // Create a new scan
        MsScan newScan = MSDKObjectBuilder.getMsScan(dataStore, scanNumber, msFunction);

        ChromatographyInfo chromInfo = MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.UNKNOWN,
                retentionTime);
        newScan.setChromatographyInfo(chromInfo);

        newScan.setDataPoints(mzValues, intensityValues, numOfDataPoints);
        newScan.setSpectrumType(spectrumType);
        newScan.setPolarity(polarity);
        newScan.setScanningRange(scanningMzRange);
        newScan.setScanDefinition(scanId);

        if (precursorMz != null) {
            IsolationInfo isolation = MSDKObjectBuilder.getIsolationInfo(Range.singleton(precursorMz), null,
                    precursorMz, precursorCharge, null);
            newScan.getIsolations().add(isolation);
        }

        // Add the scan to the file
        newRawFile.addScan(newScan);
        parsedScans++;

        // Clean the variables for next scan
        scanNumber = 0;
        scanId = null;
        polarity = null;
        scanningMzRange = null;
        msLevel = 0;
        retentionTime = 0;
        precursorMz = null;
        precursorCharge = null;
        numOfDataPoints = 0;

    }
}

From source file:net.sf.mzmine.modules.masslistmethods.ADAPchromatogrambuilder.Chromatogram.java

public void finishChromatogram() {

    int allScanNumbers[] = Ints.toArray(dataPointsMap.keySet());
    Arrays.sort(allScanNumbers);//from www  .  j  a  va2s .  com

    mz = highPointMZ;

    // Update raw data point ranges, height, rt and representative scan
    height = Double.MIN_VALUE;
    for (int i = 0; i < allScanNumbers.length; i++) {

        DataPoint mzPeak = dataPointsMap.get(allScanNumbers[i]);

        // Replace the MzPeak instance with an instance of SimpleDataPoint,
        // to reduce the memory usage. After we finish this Chromatogram, we
        // don't need the additional data provided by the MzPeak

        dataPointsMap.put(allScanNumbers[i], mzPeak);

        if (i == 0) {
            rawDataPointsIntensityRange = Range.singleton(mzPeak.getIntensity());
            rawDataPointsMZRange = Range.singleton(mzPeak.getMZ());
        } else {
            rawDataPointsIntensityRange = rawDataPointsIntensityRange
                    .span(Range.singleton(mzPeak.getIntensity()));
            rawDataPointsMZRange = rawDataPointsMZRange.span(Range.singleton(mzPeak.getMZ()));
        }

        if (height < mzPeak.getIntensity()) {
            height = mzPeak.getIntensity();
            rt = dataFile.getScan(allScanNumbers[i]).getRetentionTime();
            representativeScan = allScanNumbers[i];
        }
    }

    // Update area
    area = 0;
    for (int i = 1; i < allScanNumbers.length; i++) {
        // For area calculation, we use retention time in seconds
        double previousRT = dataFile.getScan(allScanNumbers[i - 1]).getRetentionTime() * 60d;
        double currentRT = dataFile.getScan(allScanNumbers[i]).getRetentionTime() * 60d;
        double previousHeight = dataPointsMap.get(allScanNumbers[i - 1]).getIntensity();
        double currentHeight = dataPointsMap.get(allScanNumbers[i]).getIntensity();
        area += (currentRT - previousRT) * (currentHeight + previousHeight) / 2;
    }

    // Update fragment scan
    fragmentScan = ScanUtils.findBestFragmentScan(dataFile, dataFile.getDataRTRange(1), rawDataPointsMZRange);

    if (fragmentScan > 0) {
        Scan fragmentScanObject = dataFile.getScan(fragmentScan);
        int precursorCharge = fragmentScanObject.getPrecursorCharge();
        if (precursorCharge > 0)
            this.charge = precursorCharge;
    }

    rawDataPointsRTRange = null;

    for (int scanNum : allScanNumbers) {
        double scanRt = dataFile.getScan(scanNum).getRetentionTime();
        DataPoint dp = getDataPoint(scanNum);

        if ((dp == null) || (dp.getIntensity() == 0.0))
            continue;

        if (rawDataPointsRTRange == null)
            rawDataPointsRTRange = Range.singleton(scanRt);
        else
            rawDataPointsRTRange = rawDataPointsRTRange.span(Range.singleton(scanRt));
    }

    // Discard the fields we don't need anymore
    buildingSegment = null;
    lastMzPeak = null;

}

From source file:net.sf.mzmine.modules.projectmethods.projectload.version_2_3.PeakListOpenHandler_2_3.java

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
 *      java.lang.String, java.lang.String)
 *//*from  ww w  . j  a va 2 s .c  o m*/
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {

    if (canceled)
        throw new SAXException("Parsing canceled");

    // <NAME>
    if (qName.equals(PeakListElementName_2_3.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading peak list: " + name);
        peakListName = name;
    }

    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_3.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }

    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_3.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_3.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException(
                    "Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }

    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_3.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_3.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName.equals(PeakListElementName_2_3.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_3.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] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_3.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] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <PEAK>
    if (qName.equals(PeakListElementName_2_3.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 ((peakRTRange == null) || (peakIntensityRange == null)) {
                peakRTRange = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            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);

        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status,
                representativeScan, fragmentScan, 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();
        }

        buildingRow.addPeak(dataFile, peak);

    }

    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_3.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }

    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_3.PEAK_IDENTITY.getElementName())) {
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }

    // <ROW>
    if (qName.equals(PeakListElementName_2_3.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }

    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_3.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_3.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }

    if (qName.equals(PeakListElementName_2_3.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }

}

From source file:net.sf.mzmine.modules.projectmethods.projectload.version_2_0.PeakListOpenHandler_2_0.java

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
 *      java.lang.String, java.lang.String)
 *///from  w  ww  . j  a  v  a  2 s. co  m
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {

    if (canceled)
        throw new SAXException("Parsing canceled");

    // <NAME>
    if (qName.equals(PeakListElementName_2_0.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading peak list: " + name);
        peakListName = name;
    }

    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_0.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }

    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_0.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_0.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException(
                    "Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }

    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_0.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_0.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName.equals(PeakListElementName_2_0.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_0.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] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_0.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] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <PEAK>
    if (qName.equals(PeakListElementName_2_0.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 ((peakRTRange == null) || (peakIntensityRange == null)) {
                peakRTRange = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            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);

        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status,
                representativeScan, fragmentScan, 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();
        }

        buildingRow.addPeak(dataFile, peak);

    }

    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_0.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }

    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_0.PEAK_IDENTITY.getElementName())) {
        String content = getTextOfElement();
        if (identityProperties.get(PeakIdentity.PROPERTY_NAME) == null)
            identityProperties.put(PeakIdentity.PROPERTY_NAME, content);
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }

    // <ROW>
    if (qName.equals(PeakListElementName_2_0.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }

    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_0.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_0.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }

    if (qName.equals(PeakListElementName_2_0.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }

}

From source file:net.sf.mzmine.modules.projectmethods.projectload.version_2_5.PeakListOpenHandler_2_5.java

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
 *      java.lang.String, java.lang.String)
 *///ww  w.  j  a  v  a 2s .  co m
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 peak 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 peak 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());
    }

    // <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] = (double) 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] = (double) 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 ((peakRTRange == null) || (peakIntensityRange == null)) {
                peakRTRange = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            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);

        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status,
                representativeScan, fragmentScan, 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();
        }

        buildingRow.addPeak(dataFile, peak);

    }

    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_5.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }

    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_5.PEAK_IDENTITY.getElementName())) {
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }

    // <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);
    }

}

From source file:net.sf.mzmine.project.impl.RawDataFileImpl.java

public @Nonnull Range<Double> getDataMZRange(int msLevel) {

    // check if we have this value already cached
    Range<Double> mzRange = dataMZRange.get(msLevel);
    if (mzRange != null)
        return mzRange;

    // find the value
    for (Scan scan : scans.values()) {

        // ignore scans of other ms levels
        if ((msLevel != 0) && (scan.getMSLevel() != msLevel))
            continue;

        if (mzRange == null)
            mzRange = scan.getDataPointMZRange();
        else//from  w  ww  . j av  a  2s  .c  o m
            mzRange = mzRange.span(scan.getDataPointMZRange());

    }

    // cache the value, if we found any
    if (mzRange != null)
        dataMZRange.put(msLevel, mzRange);
    else
        mzRange = Range.singleton(0.0);

    return mzRange;

}

From source file:io.github.msdk.io.mzml.MzMLConverter.java

/**
 * <p>//from w w w .j a v  a  2s  .c  o m
 * extractIsolations.
 * </p>
 *
 * @param chromatogram
 *            a {@link uk.ac.ebi.jmzml.model.mzml.Chromatogram} object.
 * @return a {@link java.util.List} object.
 */
@SuppressWarnings("null")
@Nonnull
public List<IsolationInfo> extractIsolations(uk.ac.ebi.jmzml.model.mzml.Chromatogram chromatogram) {
    if (extractChromatogramType(chromatogram) == ChromatogramType.MRM_SRM) {
        Double precursorIsolationMz = null, productIsolationMz = null, precursorActivationEnergy = null;
        ActivationType precursorActivation = ActivationType.UNKNOWN;
        ActivationInfo activationInfo = null;

        // Precursor isolation window
        String cvVal = extractCVValue(chromatogram.getPrecursor().getIsolationWindow().getCvParam(),
                MzMLCV.cvIsolationWindowTarget);
        if (!Strings.isNullOrEmpty(cvVal))
            precursorIsolationMz = Double.parseDouble(cvVal);

        // Precursor activation
        if (haveCVParam(chromatogram.getPrecursor().getActivation().getCvParam(), MzMLCV.cvActivationCID))
            precursorActivation = ActivationType.CID;

        cvVal = extractCVValue(chromatogram.getPrecursor().getActivation().getCvParam(),
                MzMLCV.cvActivationEnergy);
        if (!Strings.isNullOrEmpty(cvVal))
            precursorActivationEnergy = Double.parseDouble(cvVal);

        // Product isolation window
        cvVal = extractCVValue(chromatogram.getProduct().getIsolationWindow().getCvParam(),
                MzMLCV.cvIsolationWindowTarget);
        if (!Strings.isNullOrEmpty(cvVal))
            productIsolationMz = Double.parseDouble(cvVal);

        if (precursorActivationEnergy != null) {
            activationInfo = MSDKObjectBuilder.getActivationInfo(precursorActivationEnergy,
                    precursorActivation);
        }

        List<IsolationInfo> isolations = new ArrayList<>();
        IsolationInfo isolationInfo = null;

        if (precursorIsolationMz != null) {
            isolationInfo = MSDKObjectBuilder.getIsolationInfo(Range.singleton(precursorIsolationMz), null,
                    precursorIsolationMz, null, activationInfo);
            isolations.add(isolationInfo);
        }

        if (productIsolationMz != null) {
            isolationInfo = MSDKObjectBuilder.getIsolationInfo(Range.singleton(productIsolationMz), null,
                    productIsolationMz, null, null);
            isolations.add(isolationInfo);
        }

        return Collections.unmodifiableList(isolations);
    }

    return Collections.emptyList();

}

From source file:io.github.mzmine.modules.plots.msspectrum.MsSpectrumPlotWindowController.java

public void handleAddScan(Event e) {
    ParameterSet parameters = MZmineCore.getConfiguration().getModuleParameters(MsSpectrumPlotModule.class);
    ButtonType exitCode = parameters.showSetupDialog("Add scan");
    if (exitCode != ButtonType.OK)
        return;/*ww  w .  j  ava  2 s  . com*/

    final RawDataFilesSelection fileSelection = parameters.getParameter(MsSpectrumPlotParameters.inputFiles)
            .getValue();
    final Integer scanNumber = parameters.getParameter(MsSpectrumPlotParameters.scanNumber).getValue();
    final ScanSelection scanSelection = new ScanSelection(Range.singleton(scanNumber), null, null, null, null,
            null);
    final List<RawDataFile> dataFiles = fileSelection.getMatchingRawDataFiles();
    boolean spectrumAdded = false;
    for (RawDataFile dataFile : dataFiles) {
        for (MsScan scan : scanSelection.getMatchingScans(dataFile)) {
            String title = MsScanUtils.createSingleLineMsScanDescription(scan);
            addSpectrum(scan, title);
            spectrumAdded = true;
        }
    }
    if (!spectrumAdded) {
        MZmineGUI.displayMessage("Scan not found");
    }
}