Examples with StorableMassList net.sf.mzmine.project.impl.StorableMassList used on opensource projects

Example 1 with StorableMassList

use of net.sf.mzmine.project.impl.StorableMassList in project mzmine2 by mzmine.

the class RawDataFileSaveHandler method fillScanElement.

/**
 * Create the part of the XML document related to the scans
 *
 * @param scan
 * @param element
 */
private void fillScanElement(Scan scan, TransformerHandler hd) throws SAXException, IOException {
    // <SCAN_ID>
    AttributesImpl atts = new AttributesImpl();
    hd.startElement("", "", RawDataElementName.SCAN_ID.getElementName(), atts);
    hd.characters(String.valueOf(scan.getScanNumber()).toCharArray(), 0, String.valueOf(scan.getScanNumber()).length());
    hd.endElement("", "", RawDataElementName.SCAN_ID.getElementName());
    // <MS_LEVEL>
    hd.startElement("", "", RawDataElementName.MS_LEVEL.getElementName(), atts);
    hd.characters(String.valueOf(scan.getMSLevel()).toCharArray(), 0, String.valueOf(scan.getMSLevel()).length());
    hd.endElement("", "", RawDataElementName.MS_LEVEL.getElementName());
    if (scan.getMSLevel() >= 2) {
        // <PRECURSOR_MZ>
        hd.startElement("", "", RawDataElementName.PRECURSOR_MZ.getElementName(), atts);
        hd.characters(String.valueOf(scan.getPrecursorMZ()).toCharArray(), 0, String.valueOf(scan.getPrecursorMZ()).length());
        hd.endElement("", "", RawDataElementName.PRECURSOR_MZ.getElementName());
        // <PRECURSOR_CHARGE>
        hd.startElement("", "", RawDataElementName.PRECURSOR_CHARGE.getElementName(), atts);
        hd.characters(String.valueOf(scan.getPrecursorCharge()).toCharArray(), 0, String.valueOf(scan.getPrecursorCharge()).length());
        hd.endElement("", "", RawDataElementName.PRECURSOR_CHARGE.getElementName());
    }
    // <RETENTION_TIME>
    hd.startElement("", "", RawDataElementName.RETENTION_TIME.getElementName(), atts);
    // In the project file, retention time is represented in seconds, for
    // historical reasons
    double rt = scan.getRetentionTime() * 60d;
    hd.characters(String.valueOf(rt).toCharArray(), 0, String.valueOf(rt).length());
    hd.endElement("", "", RawDataElementName.RETENTION_TIME.getElementName());
    // <CENTROIDED>
    hd.startElement("", "", RawDataElementName.CENTROIDED.getElementName(), atts);
    hd.characters(String.valueOf(scan.getSpectrumType()).toCharArray(), 0, String.valueOf(scan.getSpectrumType()).length());
    hd.endElement("", "", RawDataElementName.CENTROIDED.getElementName());
    // <QUANTITY_DATAPOINTS>
    hd.startElement("", "", RawDataElementName.QUANTITY_DATAPOINTS.getElementName(), atts);
    hd.characters(String.valueOf((scan.getNumberOfDataPoints())).toCharArray(), 0, String.valueOf((scan.getNumberOfDataPoints())).length());
    hd.endElement("", "", RawDataElementName.QUANTITY_DATAPOINTS.getElementName());
    // <FRAGMENT_SCAN>
    if (scan.getFragmentScanNumbers() != null) {
        int[] fragmentScans = scan.getFragmentScanNumbers();
        atts.addAttribute("", "", RawDataElementName.QUANTITY.getElementName(), "CDATA", String.valueOf(fragmentScans.length));
        hd.startElement("", "", RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName(), atts);
        atts.clear();
        for (int i : fragmentScans) {
            hd.startElement("", "", RawDataElementName.FRAGMENT_SCAN.getElementName(), atts);
            hd.characters(String.valueOf(i).toCharArray(), 0, String.valueOf(i).length());
            hd.endElement("", "", RawDataElementName.FRAGMENT_SCAN.getElementName());
        }
        hd.endElement("", "", RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName());
    }
    // <MASS_LIST>
    MassList[] massLists = scan.getMassLists();
    for (MassList massList : massLists) {
        StorableMassList stMassList = (StorableMassList) massList;
        atts.addAttribute("", "", RawDataElementName.NAME.getElementName(), "CDATA", stMassList.getName());
        atts.addAttribute("", "", RawDataElementName.STORAGE_ID.getElementName(), "CDATA", String.valueOf(stMassList.getStorageID()));
        hd.startElement("", "", RawDataElementName.MASS_LIST.getElementName(), atts);
        atts.clear();
        hd.endElement("", "", RawDataElementName.MASS_LIST.getElementName());
    }
    // <POLARITY>
    hd.startElement("", "", RawDataElementName.POLARITY.getElementName(), atts);
    String pol = scan.getPolarity().toString();
    hd.characters(pol.toCharArray(), 0, pol.length());
    hd.endElement("", "", RawDataElementName.POLARITY.getElementName());
    // <SCAN_DESCRIPTION>
    hd.startElement("", "", RawDataElementName.SCAN_DESCRIPTION.getElementName(), atts);
    String scanDesc = scan.getScanDefinition();
    hd.characters(scanDesc.toCharArray(), 0, scanDesc.length());
    hd.endElement("", "", RawDataElementName.SCAN_DESCRIPTION.getElementName());
    // <SCAN_MZ_RANGE>
    hd.startElement("", "", RawDataElementName.SCAN_MZ_RANGE.getElementName(), atts);
    Range<Double> mzRange = scan.getScanningMZRange();
    String mzRangeStr = mzRange.lowerEndpoint() + "-" + mzRange.upperEndpoint();
    hd.characters(mzRangeStr.toCharArray(), 0, mzRangeStr.length());
    hd.endElement("", "", RawDataElementName.SCAN_MZ_RANGE.getElementName());
}

Example 2 with StorableMassList

use of net.sf.mzmine.project.impl.StorableMassList in project mzmine2 by mzmine.

the class RawDataFileOpenHandler_2_5 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 {
    charBuffer = new StringBuffer();
    massLists = new ArrayList<StorableMassList>();
    newRawDataFile = (RawDataFileImpl) MZmineCore.createNewFile(null);
    newRawDataFile.openDataPointsFile(scansFile);
    dataPointsOffsets = newRawDataFile.getDataPointsOffsets();
    dataPointsLengths = newRawDataFile.getDataPointsLengths();
    // Reads the XML file (raw data description)
    SAXParserFactory factory = SAXParserFactory.newInstance();
    SAXParser saxParser = factory.newSAXParser();
    saxParser.parse(is, this);
    // Adds the raw data file to MZmine
    RawDataFile rawDataFile = newRawDataFile.finishWriting();
    return rawDataFile;
}

Example 3 with StorableMassList

use of net.sf.mzmine.project.impl.StorableMassList in project mzmine2 by mzmine.

the class RawDataFileOpenHandler_2_5 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_5.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_5.QUANTITY_SCAN.getElementName())) {
        // number of scans - actually not used for anything
        Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.SCAN_ID.getElementName())) {
        scanNumber = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.STORED_DATA.getElementName())) {
        long offset = Long.parseLong(getTextOfElement());
        dataPointsOffsets.put(storedDataID, offset);
        dataPointsLengths.put(storedDataID, storedDataNumDP);
    }
    if (qName.equals(RawDataElementName_2_5.MS_LEVEL.getElementName())) {
        msLevel = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.PARENT_SCAN.getElementName())) {
        Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.POLARITY.getElementName())) {
        String txt = getTextOfElement();
        try {
            polarity = PolarityType.valueOf(txt);
        } catch (Exception e) {
            polarity = PolarityType.fromSingleChar(txt);
        }
    }
    if (qName.equals(RawDataElementName_2_5.SCAN_DESCRIPTION.getElementName())) {
        scanDescription = getTextOfElement();
    }
    if (qName.equals(RawDataElementName_2_5.SCAN_MZ_RANGE.getElementName())) {
        final String text = getTextOfElement();
        scanMZRange = RangeUtils.parseRange(text);
    }
    if (qName.equals(RawDataElementName_2_5.PRECURSOR_CHARGE.getElementName())) {
        precursorCharge = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.PRECURSOR_MZ.getElementName())) {
        precursorMZ = Double.parseDouble(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.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_5.QUANTITY_DATAPOINTS.getElementName())) {
        dataPointsNumber = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.FRAGMENT_SCAN.getElementName())) {
        fragmentScan[fragmentCount++] = Integer.parseInt(getTextOfElement());
    }
    if (qName.equals(RawDataElementName_2_5.SCAN.getElementName())) {
        StorableScan storableScan = new StorableScan(newRawDataFile, currentStorageID, dataPointsNumber, scanNumber, msLevel, retentionTime, precursorMZ, precursorCharge, fragmentScan, null, polarity, scanDescription, scanMZRange);
        try {
            newRawDataFile.addScan(storableScan);
        } catch (IOException e) {
            throw new SAXException(e);
        }
        for (StorableMassList newML : massLists) {
            newML.setScan(storableScan);
            storableScan.addMassList(newML);
        }
        // Cleanup
        massLists.clear();
        currentStorageID = -1;
        dataPointsNumber = -1;
        scanNumber = -1;
        msLevel = -1;
        retentionTime = -1;
        precursorMZ = -1;
        precursorCharge = -1;
        fragmentScan = null;
        polarity = PolarityType.UNKNOWN;
        scanDescription = "";
        scanMZRange = null;
    }
}

Example 4 with StorableMassList

use of net.sf.mzmine.project.impl.StorableMassList in project mzmine2 by mzmine.

the class RawDataFileOpenHandler_2_5 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_5.QUANTITY_FRAGMENT_SCAN.getElementName())) {
        numberOfFragments = Integer.parseInt(attrs.getValue(RawDataElementName_2_5.QUANTITY.getElementName()));
        if (numberOfFragments > 0) {
            fragmentScan = new int[numberOfFragments];
            fragmentCount = 0;
        }
    }
    if (qName.equals(RawDataElementName_2_5.SCAN.getElementName())) {
        currentStorageID = Integer.parseInt(attrs.getValue(RawDataElementName_2_5.STORAGE_ID.getElementName()));
    }
    if (qName.equals(RawDataElementName_2_5.STORED_DATA.getElementName())) {
        storedDataID = Integer.parseInt(attrs.getValue(RawDataElementName_2_5.STORAGE_ID.getElementName()));
        storedDataNumDP = Integer.parseInt(attrs.getValue(RawDataElementName_2_5.QUANTITY_DATAPOINTS.getElementName()));
    }
    if (qName.equals(RawDataElementName_2_5.MASS_LIST.getElementName())) {
        String name = attrs.getValue(RawDataElementName_2_5.NAME.getElementName());
        int storageID = Integer.parseInt(attrs.getValue(RawDataElementName_2_5.STORAGE_ID.getElementName()));
        StorableMassList newML = new StorableMassList(newRawDataFile, storageID, name, null);
        massLists.add(newML);
    }
}