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

Example 1 with SimpleMassList

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

the class MassDetectionTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    // make arrays to contain everything you need
    ArrayList<Integer> pointsInScans = new ArrayList<>();
    ArrayList<Double> allMZ = new ArrayList<>();
    ArrayList<Double> allIntensities = new ArrayList<>();
    // idecies of full mass list where scan starts?
    ArrayList<Integer> startIndex = new ArrayList<>();
    ArrayList<Double> scanAcquisitionTime = new ArrayList<>();
    // XCMS needs this one
    ArrayList<Double> totalIntensity = new ArrayList<>();
    double curTotalIntensity;
    int lastPointCount = 0;
    startIndex.add(0);
    try {
        setStatus(TaskStatus.PROCESSING);
        logger.info("Started mass detector on " + dataFile);
        final Scan[] scans = scanSelection.getMatchingScans(dataFile);
        totalScans = scans.length;
        // Process scans one by one
        for (Scan scan : scans) {
            if (isCanceled())
                return;
            MassDetector detector = massDetector.getModule();
            DataPoint[] mzPeaks = detector.getMassValues(scan, massDetector.getParameterSet());
            SimpleMassList newMassList = new SimpleMassList(name, scan, mzPeaks);
            // Add new mass list to the scan
            scan.addMassList(newMassList);
            if (this.saveToCDF) {
                curTotalIntensity = 0;
                for (int a = 0; a < mzPeaks.length; a++) {
                    DataPoint curMzPeak = mzPeaks[a];
                    allMZ.add(curMzPeak.getMZ());
                    allIntensities.add(curMzPeak.getIntensity());
                    curTotalIntensity += curMzPeak.getIntensity();
                }
                scanAcquisitionTime.add(scan.getRetentionTime());
                pointsInScans.add(0);
                startIndex.add(mzPeaks.length + lastPointCount);
                totalIntensity.add(curTotalIntensity);
                lastPointCount = mzPeaks.length + lastPointCount;
            }
            processedScans++;
        }
        // Update the GUI with all new mass lists
        MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore.getProjectManager().getCurrentProject();
        final RawDataTreeModel treeModel = project.getRawDataTreeModel();
        treeModel.updateGUIWithNewObjects();
        ;
        if (this.saveToCDF) {
            // ************** write mass list *******************************
            final String outFileNamePath = outFilename.getPath();
            logger.info("Saving mass detector results to netCDF file " + outFileNamePath);
            NetcdfFileWriter writer = NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFileNamePath, null);
            Dimension dim_massValues = writer.addDimension(null, "mass_values", allMZ.size());
            Dimension dim_intensityValues = writer.addDimension(null, "intensity_values", allIntensities.size());
            Dimension dim_scanIndex = writer.addDimension(null, "scan_index", startIndex.size() - 1);
            Dimension dim_scanAcquisitionTime = writer.addDimension(null, "scan_acquisition_time", scanAcquisitionTime.size());
            Dimension dim_totalIntensity = writer.addDimension(null, "total_intensity", totalIntensity.size());
            Dimension dim_pointsInScans = writer.addDimension(null, "point_count", pointsInScans.size());
            // add dimensions to list
            List<Dimension> dims = new ArrayList<>();
            dims.add(dim_massValues);
            dims.add(dim_intensityValues);
            dims.add(dim_scanIndex);
            dims.add(dim_scanAcquisitionTime);
            dims.add(dim_totalIntensity);
            dims.add(dim_pointsInScans);
            // make the variables that contain the actual data I think.
            Variable var_massValues = writer.addVariable(null, "mass_values", DataType.DOUBLE, "mass_values");
            Variable var_intensityValues = writer.addVariable(null, "intensity_values", DataType.DOUBLE, "intensity_values");
            Variable var_scanIndex = writer.addVariable(null, "scan_index", DataType.INT, "scan_index");
            Variable var_scanAcquisitionTime = writer.addVariable(null, "scan_acquisition_time", DataType.DOUBLE, "scan_acquisition_time");
            Variable var_totalIntensity = writer.addVariable(null, "total_intensity", DataType.DOUBLE, "total_intensity");
            Variable var_pointsInScans = writer.addVariable(null, "point_count", DataType.INT, "point_count");
            var_massValues.addAttribute(new Attribute("units", "M/Z"));
            var_intensityValues.addAttribute(new Attribute("units", "Arbitrary Intensity Units"));
            var_scanIndex.addAttribute(new Attribute("units", "index"));
            var_scanAcquisitionTime.addAttribute(new Attribute("units", "seconds"));
            var_totalIntensity.addAttribute(new Attribute("units", "Arbitrary Intensity Units"));
            var_pointsInScans.addAttribute(new Attribute("units", "count"));
            var_massValues.addAttribute(new Attribute("scale_factor", 1.0));
            var_intensityValues.addAttribute(new Attribute("scale_factor", 1.0));
            var_scanIndex.addAttribute(new Attribute("scale_factor", 1.0));
            var_scanAcquisitionTime.addAttribute(new Attribute("scale_factor", 1.0));
            var_totalIntensity.addAttribute(new Attribute("scale_factor", 1.0));
            var_pointsInScans.addAttribute(new Attribute("scale_factor", 1.0));
            // create file
            writer.create();
            ArrayDouble.D1 arr_massValues = new ArrayDouble.D1(dim_massValues.getLength());
            ArrayDouble.D1 arr_intensityValues = new ArrayDouble.D1(dim_intensityValues.getLength());
            ArrayDouble.D1 arr_scanIndex = new ArrayDouble.D1(dim_scanIndex.getLength());
            ArrayDouble.D1 arr_scanAcquisitionTime = new ArrayDouble.D1(dim_scanAcquisitionTime.getLength());
            ArrayDouble.D1 arr_totalIntensity = new ArrayDouble.D1(dim_totalIntensity.getLength());
            ArrayDouble.D1 arr_pointsInScans = new ArrayDouble.D1(dim_pointsInScans.getLength());
            for (int i = 0; i < allMZ.size(); i++) {
                arr_massValues.set(i, allMZ.get(i));
                arr_intensityValues.set(i, allIntensities.get(i));
            }
            int i = 0;
            for (; i < scanAcquisitionTime.size(); i++) {
                arr_scanAcquisitionTime.set(i, scanAcquisitionTime.get(i) * 60);
                arr_pointsInScans.set(i, pointsInScans.get(i));
                arr_scanIndex.set(i, startIndex.get(i));
                arr_totalIntensity.set(i, totalIntensity.get(i));
            }
            // arr_scanIndex.set(i,startIndex.get(i));
            // For tiny test file
            // arr_intensityValues .set(0,200);
            // arr_scanIndex .set(0,0);
            // arr_scanAcquisitionTime .set(0,10);
            // arr_totalIntensity .set(0,200);
            // arr_pointsInScans .set(0,0);
            // arr_intensityValues .set(1,300);
            // arr_scanIndex .set(1,1);
            // arr_scanAcquisitionTime .set(1,20);
            // arr_totalIntensity .set(1,300);
            // arr_pointsInScans .set(1,0);
            writer.write(var_massValues, arr_massValues);
            writer.write(var_intensityValues, arr_intensityValues);
            writer.write(var_scanIndex, arr_scanIndex);
            writer.write(var_scanAcquisitionTime, arr_scanAcquisitionTime);
            writer.write(var_totalIntensity, arr_totalIntensity);
            writer.write(var_pointsInScans, arr_pointsInScans);
            writer.close();
        }
    } catch (Exception e) {
        e.printStackTrace();
        setErrorMessage(e.getMessage());
        setStatus(TaskStatus.ERROR);
    }
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished mass detector on " + dataFile);
}

Example 2 with SimpleMassList

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

the class ShoulderPeaksFilterTask method run.

/**
 * @see Runnable#run()
 */
public void run() {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Started mass filter on " + dataFile);
    scanNumbers = dataFile.getScanNumbers();
    totalScans = scanNumbers.length;
    // Check if we have at least one scan with a mass list of given name
    boolean haveMassList = false;
    for (int i = 0; i < totalScans; i++) {
        Scan scan = dataFile.getScan(scanNumbers[i]);
        MassList massList = scan.getMassList(massListName);
        if (massList != null) {
            haveMassList = true;
            break;
        }
    }
    if (!haveMassList) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage(dataFile.getName() + " has no mass list called '" + massListName + "'");
        return;
    }
    // Process all scans
    for (int i = 0; i < totalScans; i++) {
        if (isCanceled())
            return;
        Scan scan = dataFile.getScan(scanNumbers[i]);
        MassList massList = scan.getMassList(massListName);
        // Skip those scans which do not have a mass list of given name
        if (massList == null) {
            processedScans++;
            continue;
        }
        DataPoint[] mzPeaks = massList.getDataPoints();
        DataPoint[] newMzPeaks = ShoulderPeaksFilter.filterMassValues(mzPeaks, parameters);
        SimpleMassList newMassList = new SimpleMassList(massListName + " " + suffix, scan, newMzPeaks);
        scan.addMassList(newMassList);
        // Remove old mass list
        if (autoRemove)
            scan.removeMassList(massList);
        processedScans++;
    }
    setStatus(TaskStatus.FINISHED);
    logger.info("Finished shoulder peaks filter on " + dataFile);
}

Example 3 with SimpleMassList

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

the class RawDataFileOpenHandler_2_3 method startElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String,
 *      java.lang.String, org.xml.sax.Attributes)
 */
public void startElement(String namespaceURI, String lName, String qName, Attributes attrs) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // This will remove any remaining characters from previous elements
    getTextOfElement();
    if (qName.equals(RawDataElementName_2_3.QUANTITY_FRAGMENT_SCAN.getElementName())) {
        numberOfFragments = Integer.parseInt(attrs.getValue(RawDataElementName_2_3.QUANTITY.getElementName()));
        if (numberOfFragments > 0) {
            fragmentScan = new int[numberOfFragments];
            fragmentCount = 0;
        }
    }
    if (qName.equals(RawDataElementName_2_3.MASS_LIST.getElementName())) {
        String name = attrs.getValue(RawDataElementName_2_3.NAME.getElementName());
        SimpleMassList newML = new SimpleMassList(name, null, null);
        currentMassLists.add(newML);
    }
}

Example 4 with SimpleMassList

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

the class RawDataFileOpenHandler_2_3 method endElement.

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
 *      java.lang.String)
 */
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
    if (canceled)
        throw new SAXException("Parsing canceled");
    // <NAME>
    if (qName.equals(RawDataElementName_2_3.NAME.getElementName())) {
        // Adds the scan file and the name to the new raw data file
        String name = getTextOfElement();
        logger.info("Loading raw data file: " + name);
        newRawDataFile.setName(name);
    }
    if (qName.equals(RawDataElementName_2_3.QUANTITY_SCAN.getElementName())) {
        // number of scans - actually not used for anything
        Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.SCAN_ID.getElementName())) {
        scanNumber = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.MS_LEVEL.getElementName())) {
        msLevel = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.PARENT_SCAN.getElementName())) {
        Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.PRECURSOR_MZ.getElementName())) {
        precursorMZ = Double.parseDouble(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.PRECURSOR_CHARGE.getElementName())) {
        precursorCharge = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.RETENTION_TIME.getElementName())) {
        // Before MZmine 2.6 retention time was saved in seconds, but now we
        // use
        // minutes, so we need to divide by 60
        retentionTime = Double.parseDouble(getTextOfElement()) / 60d;
    }
    if (qName.equals(RawDataElementName_2_3.CENTROIDED.getElementName())) {
        boolean centroided = Boolean.parseBoolean(getTextOfElement());
        if (centroided)
            spectrumType = MassSpectrumType.CENTROIDED;
        else
            spectrumType = MassSpectrumType.PROFILE;
    }
    if (qName.equals(RawDataElementName_2_3.QUANTITY_DATAPOINTS.getElementName())) {
        dataPointsNumber = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.FRAGMENT_SCAN.getElementName())) {
        fragmentScan[fragmentCount++] = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_3.MASS_LIST.getElementName())) {
        char[] encodedDataPoints = getTextOfElement().toCharArray();
        DataPoint[] dataPoints = ScanUtils.decodeDataPointsBase64(encodedDataPoints);
        SimpleMassList newML = currentMassLists.get(currentMassLists.size() - 1);
        newML.setDataPoints(dataPoints);
    }
    if (qName.equals(RawDataElementName_2_3.SCAN.getElementName())) {
        try {
            int newStorageID = 1;
            TreeMap<Integer, Long> dataPointsOffsets = newRawDataFile.getDataPointsOffsets();
            TreeMap<Integer, Integer> dataPointsLengths = newRawDataFile.getDataPointsLengths();
            if (!dataPointsOffsets.isEmpty())
                newStorageID = dataPointsOffsets.lastKey().intValue() + 1;
            StorableScan storableScan = new StorableScan(newRawDataFile, newStorageID, dataPointsNumber, scanNumber, msLevel, retentionTime, precursorMZ, precursorCharge, fragmentScan, spectrumType, PolarityType.UNKNOWN, "", null);
            newRawDataFile.addScan(storableScan);
            dataPointsOffsets.put(newStorageID, storageFileOffset);
            dataPointsLengths.put(newStorageID, dataPointsNumber);
            for (SimpleMassList newML : currentMassLists) {
                newML.setScan(storableScan);
            }
            allMassLists.addAll(currentMassLists);
            currentMassLists.clear();
        } catch (IOException e) {
            throw new SAXException(e);
        }
        storageFileOffset += dataPointsNumber * 4 * 2;
    }
}

Example 5 with SimpleMassList

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

the class RawDataFileOpenHandler_2_3 method readRawDataFile.

/**
 * Extract the scan file and copies it into the temporary folder. Create a new raw data file using
 * the information from the XML raw data description file
 *
 * @param Name raw data file name
 * @throws SAXException
 * @throws ParserConfigurationException
 */
public RawDataFile readRawDataFile(InputStream is, File scansFile) throws IOException, ParserConfigurationException, SAXException {
    storageFileOffset = 0;
    charBuffer = new StringBuffer();
    currentMassLists = new ArrayList<SimpleMassList>();
    allMassLists = new ArrayList<SimpleMassList>();
    newRawDataFile = (RawDataFileImpl) MZmineCore.createNewFile(null);
    newRawDataFile.openDataPointsFile(scansFile);
    // Reads the XML file (raw data description)
    SAXParserFactory factory = SAXParserFactory.newInstance();
    SAXParser saxParser = factory.newSAXParser();
    saxParser.parse(is, this);
    // instead of being part of the data points file.
    for (SimpleMassList ml : allMassLists) {
        Scan s = ml.getScan();
        s.addMassList(ml);
    }
    RawDataFile rawDataFile = newRawDataFile.finishWriting();
    return rawDataFile;
}