javax.xml.transform.sax.TransformerHandler#endElement

Source File: PeakListSaveHandler.java From mzmine3 with GNU General Public License v2.0

6 votes

/**
 * Add the peak identity information into the XML document
 *
 * @param identity
 * @param element
 */
private void fillIdentityElement(PeakIdentity identity, TransformerHandler hd)
    throws SAXException {

  AttributesImpl atts = new AttributesImpl();

  Map<String, String> idProperties = identity.getAllProperties();

  for (Entry<String, String> property : idProperties.entrySet()) {
    String propertyValue = property.getValue();
    atts.clear();
    atts.addAttribute("", "", PeakListElementName.NAME.getElementName(), "CDATA",
        property.getKey());

    hd.startElement("", "", PeakListElementName.IDPROPERTY.getElementName(), atts);
    hd.characters(propertyValue.toCharArray(), 0, propertyValue.length());
    hd.endElement("", "", PeakListElementName.IDPROPERTY.getElementName());
  }

}

Source File: PeakListSaveHandler.java From mzmine2 with GNU General Public License v2.0

6 votes

private void fillInformationElement(PeakInformation information, TransformerHandler hd)
    throws SAXException {
  if (information == null)
    return;

  AttributesImpl atts = new AttributesImpl();

  for (Entry<String, String> property : information.getAllProperties().entrySet()) {
    String value = property.getValue();

    atts.clear();
    atts.addAttribute("", "", PeakListElementName.NAME.getElementName(), "CDATA",
        property.getKey());

    hd.startElement("", "", PeakListElementName.INFO_PROPERTY.getElementName(), atts);
    hd.characters(property.getValue().toCharArray(), 0, value.length());
    hd.endElement("", "", PeakListElementName.INFO_PROPERTY.getElementName());
  }
}

Source File: PeakListSaveHandler.java From mzmine2 with GNU General Public License v2.0

6 votes

/**
 * Add the peak identity information into the XML document
 * 
 * @param identity
 * @param element
 */
private void fillIdentityElement(PeakIdentity identity, TransformerHandler hd)
    throws SAXException {

  AttributesImpl atts = new AttributesImpl();

  Map<String, String> idProperties = identity.getAllProperties();

  for (Entry<String, String> property : idProperties.entrySet()) {
    String propertyValue = property.getValue();
    atts.clear();
    atts.addAttribute("", "", PeakListElementName.NAME.getElementName(), "CDATA",
        property.getKey());

    hd.startElement("", "", PeakListElementName.IDPROPERTY.getElementName(), atts);
    hd.characters(propertyValue.toCharArray(), 0, propertyValue.length());
    hd.endElement("", "", PeakListElementName.IDPROPERTY.getElementName());
  }

}

Source File: Bug6451633.java From openjdk-jdk9 with GNU General Public License v2.0

6 votes

@Test
public void test() throws Exception {
    TransformerHandler th = ((SAXTransformerFactory) TransformerFactory.newInstance()).newTransformerHandler();

    DOMResult result = new DOMResult();
    th.setResult(result);

    th.startDocument();
    th.startElement("", "root", "root", new AttributesImpl());
    th.characters(new char[0], 0, 0);
    th.endElement("", "root", "root");
    th.endDocument();

    // there's no point in having empty text --- we should remove it
    Assert.assertEquals(0, ((Document) result.getNode()).getDocumentElement().getChildNodes().getLength());
}

Source File: PeakListSaveHandler.java From mzmine3 with GNU General Public License v2.0

5 votes

private void fillIsotopePatternElement(IsotopePattern isotopePattern, TransformerHandler hd)
    throws SAXException, IOException {

  AttributesImpl atts = new AttributesImpl();

  DataPoint isotopes[] = isotopePattern.getDataPoints();

  for (DataPoint isotope : isotopes) {
    hd.startElement("", "", PeakListElementName.ISOTOPE.getElementName(), atts);
    String isotopeString = isotope.getMZ() + ":" + isotope.getIntensity();
    hd.characters(isotopeString.toCharArray(), 0, isotopeString.length());
    hd.endElement("", "", PeakListElementName.ISOTOPE.getElementName());
  }
}

Source File: PeakListSaveHandler.java From mzmine3 with GNU General Public License v2.0

5 votes

private void fillAllMS2FragmentScanNumbers(int[] scanNumbers, TransformerHandler hd)
    throws SAXException, IOException {
  AttributesImpl atts = new AttributesImpl();
  if (scanNumbers != null) {
    for (int scan : scanNumbers) {
      hd.startElement("", "", PeakListElementName.ALL_MS2_FRAGMENT_SCANS.getElementName(), atts);
      hd.characters(String.valueOf(scan).toCharArray(), 0, String.valueOf(scan).length());
      hd.endElement("", "", PeakListElementName.ALL_MS2_FRAGMENT_SCANS.getElementName());
    }
  }
}

Source File: IvyArtifactReport.java From ant-ivy with Apache License 2.0

5 votes

private void writeRetrieveLocation(TransformerHandler saxHandler, String artifactDestPath)
        throws SAXException {
    artifactDestPath = removeLeadingPath(getProject().getBaseDir(), new File(artifactDestPath));

    saxHandler.startElement(null, "retrieve-location", "retrieve-location",
        new AttributesImpl());
    char[] artifactDestPathAsChars = artifactDestPath.replace('\\', '/').toCharArray();
    saxHandler.characters(artifactDestPathAsChars, 0, artifactDestPathAsChars.length);
    saxHandler.endElement(null, "retrieve-location", "retrieve-location");
}

Source File: IvyArtifactReport.java From ant-ivy with Apache License 2.0

5 votes

private void writeCacheLocationIfPresent(RepositoryCacheManager cache,
        TransformerHandler saxHandler, ArtifactDownloadReport artifact) throws SAXException {
    File archiveInCache = artifact.getLocalFile();

    if (archiveInCache != null) {
        saxHandler.startElement(null, "cache-location", "cache-location", new AttributesImpl());
        char[] archiveInCacheAsChars = archiveInCache.getPath().replace('\\', '/')
                .toCharArray();
        saxHandler.characters(archiveInCacheAsChars, 0, archiveInCacheAsChars.length);
        saxHandler.endElement(null, "cache-location", "cache-location");
    }
}

Source File: PeakListSaveHandler.java From mzmine2 with GNU General Public License v2.0

5 votes

private void fillAllMS2FragmentScanNumbers(int[] scanNumbers, TransformerHandler hd)
    throws SAXException, IOException {
  AttributesImpl atts = new AttributesImpl();
  if (scanNumbers != null) {
    for (int scan : scanNumbers) {
      hd.startElement("", "", PeakListElementName.ALL_MS2_FRAGMENT_SCANS.getElementName(), atts);
      hd.characters(String.valueOf(scan).toCharArray(), 0, String.valueOf(scan).length());
      hd.endElement("", "", PeakListElementName.ALL_MS2_FRAGMENT_SCANS.getElementName());
    }
  }
}

Source File: XmlWriter.java From CloverETL-Engine with GNU Lesser General Public License v2.1

5 votes

private void createFooter(OutputStream os, TransformerHandler hd) throws TransformerConfigurationException, SAXException, IOException {
	try {
		//if (recordsPerFile!=1){
		if (this.useRootElement){
			 String root = (rootElement!=null && rootElement.length()>0) ? rootElement : DEFAULT_ROOT_ELEMENT; 
			 hd.endElement(rootDefaultNamespace, getLocalName(root), root);
			 for (String prefix : namespaces.keySet())
				 hd.endPrefixMapping(prefix);
		}
		hd.endDocument();
	} finally {
		 os.close();
	}
}

Source File: GanttOptions.java From ganttproject with GNU General Public License v3.0

5 votes

private void saveRoleSets(TransformerHandler handler) throws TransformerFactoryConfigurationError, SAXException {
  RoleSet[] roleSets = getRoleManager().getRoleSets();
  for (int i = 0; i < roleSets.length; i++) {
    AttributesImpl attrs = new AttributesImpl();
    attrs.addAttribute("", "roleset-name", "roleset-name", "CDATA", roleSets[i].getName());
    handler.startElement("", "roles", "roles", attrs);
    saveRoles(roleSets[i], handler);
    handler.endElement("", "roles", "roles");
  }
}

Source File: XmlTools.java From MyBox with Apache License 2.0

4 votes

public static void iccHeaderXml(LinkedHashMap<String, Object> header, File file) {
    if (header == null || file == null) {
        return;
    }
    try {
        SAXTransformerFactory sf = (SAXTransformerFactory) SAXTransformerFactory.newInstance();
        TransformerHandler handler = sf.newTransformerHandler();
        Transformer transformer = handler.getTransformer();
        transformer.setOutputProperty(OutputKeys.STANDALONE, "yes");
        transformer.setOutputProperty(OutputKeys.ENCODING, "utf-8");
        transformer.setOutputProperty(OutputKeys.INDENT, "yes");
        Result result = new StreamResult(new BufferedOutputStream(new FileOutputStream(file)));
        handler.setResult(result);
        handler.startDocument();
        AttributesImpl attr = new AttributesImpl();
        handler.startElement("", "", "IccProfile", attr);
        handler.startElement("", "", "Header", attr);

        handler.startElement("", "", "PreferredCMMType", attr);
        String stringV = (String) header.get("CMMType");
        handler.characters(stringV.toCharArray(), 0, stringV.length());
        handler.endElement("", "", "PreferredCMMType");

        handler.startElement("", "", "PCSIlluminant", attr);
        attr.clear();
        attr.addAttribute("", "", "X", "", header.get("x") + "");
        attr.addAttribute("", "", "Y", "", header.get("y") + "");
        attr.addAttribute("", "", "Z", "", header.get("z") + "");
        handler.startElement("", "", "XYZNumber", attr);
        handler.endElement("", "", "XYZNumber");
        handler.endElement("", "", "PCSIlluminant");

        handler.endElement("", "", "Header");
        handler.endElement("", "", "IccProfile");

        handler.endDocument();

    } catch (Exception e) {

    }

}

Source File: SAXGenerator.java From AndroidPixelDimenGenerator with Apache License 2.0

4 votes

public void generate(Values values) throws IOException {
    File dimenFile = values.dimenFile;
    FileOutputStream fos = new FileOutputStream(dimenFile);
    StreamResult result = new StreamResult(fos);
    SAXTransformerFactory sff = (SAXTransformerFactory) SAXTransformerFactory.newInstance();
    TransformerHandler th = null;
    try {
        th = sff.newTransformerHandler();
        Transformer transformer = th.getTransformer();
        transformer.setOutputProperty(OutputKeys.ENCODING, "utf-8");
        transformer.setOutputProperty(OutputKeys.INDENT, "yes");

        th.setResult(result);

        th.startDocument();

        AttributesImpl attr = new AttributesImpl();
        char[] space = "\n".toCharArray();
        th.characters(space, 0, space.length);
        th.startElement("", "", "resources", attr);

        List<Dimen> dimens = values.dimens;
        char[] spaceChar = "\n    ".toCharArray();
        for (Dimen dimen : dimens) {
            //white space
            th.characters(spaceChar, 0, spaceChar.length);
            //name attr
            attr.addAttribute("", "", "name", String.class.getName(), dimen.name);
            th.startElement("", "", "dimen", attr);
            char[] valueChars = String.format("%spx", dimen.value).toCharArray();
            th.characters(valueChars, 0, valueChars.length);
            th.endElement("", "", "dimen");
        }

        th.endElement("", "", "resources");
        th.endDocument();

    } catch (TransformerConfigurationException | SAXException e) {
        e.printStackTrace();
    } finally {
        fos.close();
    }
}

Source File: PeakListSaveHandler.java From mzmine3 with GNU General Public License v2.0

4 votes

/**
 * Add the peaks information into the XML document
 *
 * @param peak
 * @param element
 * @param dataFileID
 * @throws IOException
 */
private void fillPeakElement(Feature peak, TransformerHandler hd)
    throws SAXException, IOException {
  AttributesImpl atts = new AttributesImpl();

  // <REPRESENTATIVE_SCAN>
  hd.startElement("", "", PeakListElementName.REPRESENTATIVE_SCAN.getElementName(), atts);
  hd.characters(String.valueOf(peak.getRepresentativeScanNumber()).toCharArray(), 0,
      String.valueOf(peak.getRepresentativeScanNumber()).length());
  hd.endElement("", "", PeakListElementName.REPRESENTATIVE_SCAN.getElementName());

  // <FRAGMENT_SCAN>
  hd.startElement("", "", PeakListElementName.FRAGMENT_SCAN.getElementName(), atts);
  hd.characters(String.valueOf(peak.getMostIntenseFragmentScanNumber()).toCharArray(), 0,
      String.valueOf(peak.getMostIntenseFragmentScanNumber()).length());
  hd.endElement("", "", PeakListElementName.FRAGMENT_SCAN.getElementName());

  // <ALL_MS2_FRAGMENT_SCANS>
  fillAllMS2FragmentScanNumbers(peak.getAllMS2FragmentScanNumbers(), hd);

  int scanNumbers[] = peak.getScanNumbers();

  // <ISOTOPE_PATTERN>
  IsotopePattern isotopePattern = peak.getIsotopePattern();
  if (isotopePattern != null) {
    atts.addAttribute("", "", PeakListElementName.STATUS.getElementName(), "CDATA",
        String.valueOf(isotopePattern.getStatus()));
    atts.addAttribute("", "", PeakListElementName.DESCRIPTION.getElementName(), "CDATA",
        isotopePattern.getDescription());
    hd.startElement("", "", PeakListElementName.ISOTOPE_PATTERN.getElementName(), atts);
    atts.clear();

    fillIsotopePatternElement(isotopePattern, hd);

    hd.endElement("", "", PeakListElementName.ISOTOPE_PATTERN.getElementName());

  }

  // <MZPEAK>
  atts.addAttribute("", "", PeakListElementName.QUANTITY.getElementName(), "CDATA",
      String.valueOf(scanNumbers.length));
  hd.startElement("", "", PeakListElementName.MZPEAKS.getElementName(), atts);
  atts.clear();

  // <SCAN_ID> <MASS> <HEIGHT>
  ByteArrayOutputStream byteScanStream = new ByteArrayOutputStream();
  DataOutputStream dataScanStream = new DataOutputStream(byteScanStream);

  ByteArrayOutputStream byteMassStream = new ByteArrayOutputStream();
  DataOutputStream dataMassStream = new DataOutputStream(byteMassStream);

  ByteArrayOutputStream byteHeightStream = new ByteArrayOutputStream();
  DataOutputStream dataHeightStream = new DataOutputStream(byteHeightStream);

  float mass, height;
  for (int scan : scanNumbers) {
    dataScanStream.writeInt(scan);
    dataScanStream.flush();
    DataPoint mzPeak = peak.getDataPoint(scan);
    if (mzPeak != null) {
      mass = (float) mzPeak.getMZ();
      height = (float) mzPeak.getIntensity();
    } else {
      mass = 0f;
      height = 0f;
    }
    dataMassStream.writeFloat(mass);
    dataMassStream.flush();
    dataHeightStream.writeFloat(height);
    dataHeightStream.flush();
  }

  byte[] bytes = Base64.encode(byteScanStream.toByteArray());
  hd.startElement("", "", PeakListElementName.SCAN_ID.getElementName(), atts);
  String sbytes = new String(bytes);
  hd.characters(sbytes.toCharArray(), 0, sbytes.length());
  hd.endElement("", "", PeakListElementName.SCAN_ID.getElementName());

  bytes = Base64.encode(byteMassStream.toByteArray());
  hd.startElement("", "", PeakListElementName.MZ.getElementName(), atts);
  sbytes = new String(bytes);
  hd.characters(sbytes.toCharArray(), 0, sbytes.length());
  hd.endElement("", "", PeakListElementName.MZ.getElementName());

  bytes = Base64.encode(byteHeightStream.toByteArray());
  hd.startElement("", "", PeakListElementName.HEIGHT.getElementName(), atts);
  sbytes = new String(bytes);
  hd.characters(sbytes.toCharArray(), 0, sbytes.length());
  hd.endElement("", "", PeakListElementName.HEIGHT.getElementName());

  hd.endElement("", "", PeakListElementName.MZPEAKS.getElementName());
}

Source File: PeakListSaveHandler.java From mzmine2 with GNU General Public License v2.0

4 votes

/**
 * Add the row information into the XML document
 * 
 * @param row
 * @param element
 * @throws IOException
 */
private void fillRowElement(PeakListRow row, TransformerHandler hd)
    throws SAXException, IOException {

  // <PEAK_IDENTITY>
  PeakIdentity preferredIdentity = row.getPreferredPeakIdentity();
  PeakIdentity[] identities = row.getPeakIdentities();
  AttributesImpl atts = new AttributesImpl();

  for (int i = 0; i < identities.length; i++) {

    if (canceled)
      return;

    atts.addAttribute("", "", PeakListElementName.ID.getElementName(), "CDATA",
        String.valueOf(i));
    atts.addAttribute("", "", PeakListElementName.PREFERRED.getElementName(), "CDATA",
        String.valueOf(identities[i] == preferredIdentity));
    hd.startElement("", "", PeakListElementName.PEAK_IDENTITY.getElementName(), atts);
    fillIdentityElement(identities[i], hd);
    hd.endElement("", "", PeakListElementName.PEAK_IDENTITY.getElementName());
  }

  // <PEAK_INFORMATION>

  // atts.clear();

  if (canceled)
    return;

  // atts.addAttribute("", "", PeakListElementName.ID.getElementName(),
  // "CDATA", "INFORMATION");
  hd.startElement("", "", PeakListElementName.PEAK_INFORMATION.getElementName(), atts);
  fillInformationElement(row.getPeakInformation(), hd);
  hd.endElement("", "", PeakListElementName.PEAK_INFORMATION.getElementName());

  // <PEAK>
  Feature[] peaks = row.getPeaks();
  for (Feature p : peaks) {
    if (canceled)
      return;

    atts.clear();
    String dataFileID = dataFilesIDMap.get(p.getDataFile());
    atts.addAttribute("", "", PeakListElementName.COLUMN.getElementName(), "CDATA", dataFileID);
    atts.addAttribute("", "", PeakListElementName.MZ.getElementName(), "CDATA",
        String.valueOf(p.getMZ()));
    // In the project file, retention time is represented in seconds,
    // for historical reasons
    double rt = p.getRT() * 60d;
    atts.addAttribute("", "", PeakListElementName.RT.getElementName(), "CDATA",
        String.valueOf(rt));
    atts.addAttribute("", "", PeakListElementName.HEIGHT.getElementName(), "CDATA",
        String.valueOf(p.getHeight()));
    atts.addAttribute("", "", PeakListElementName.AREA.getElementName(), "CDATA",
        String.valueOf(p.getArea()));
    atts.addAttribute("", "", PeakListElementName.STATUS.getElementName(), "CDATA",
        p.getFeatureStatus().toString());
    atts.addAttribute("", "", PeakListElementName.CHARGE.getElementName(), "CDATA",
        String.valueOf(p.getCharge()));
    atts.addAttribute("", "", PeakListElementName.PARENT_CHROMATOGRAM_ROW_ID.getElementName(), "CDATA",
        p.getParentChromatogramRowID() != null ? String.valueOf(p.getParentChromatogramRowID()) : "");
    hd.startElement("", "", PeakListElementName.PEAK.getElementName(), atts);

    fillPeakElement(p, hd);
    hd.endElement("", "", PeakListElementName.PEAK.getElementName());
  }

}

Source File: PeakListSaveHandler.java From mzmine3 with GNU General Public License v2.0

4 votes

/**
 * Add the row information into the XML document
 *
 * @param row
 * @param element
 * @throws IOException
 */
private void fillRowElement(PeakListRow row, TransformerHandler hd)
    throws SAXException, IOException {

  // <PEAK_IDENTITY>
  PeakIdentity preferredIdentity = row.getPreferredPeakIdentity();
  PeakIdentity[] identities = row.getPeakIdentities();
  AttributesImpl atts = new AttributesImpl();

  for (int i = 0; i < identities.length; i++) {

    if (canceled)
      return;

    atts.addAttribute("", "", PeakListElementName.ID.getElementName(), "CDATA",
        String.valueOf(i));
    atts.addAttribute("", "", PeakListElementName.PREFERRED.getElementName(), "CDATA",
        String.valueOf(identities[i] == preferredIdentity));
    hd.startElement("", "", PeakListElementName.PEAK_IDENTITY.getElementName(), atts);
    fillIdentityElement(identities[i], hd);
    hd.endElement("", "", PeakListElementName.PEAK_IDENTITY.getElementName());
  }

  // <PEAK_INFORMATION>

  // atts.clear();

  if (canceled)
    return;

  // atts.addAttribute("", "", PeakListElementName.ID.getElementName(),
  // "CDATA", "INFORMATION");
  hd.startElement("", "", PeakListElementName.PEAK_INFORMATION.getElementName(), atts);
  fillInformationElement(row.getPeakInformation(), hd);
  hd.endElement("", "", PeakListElementName.PEAK_INFORMATION.getElementName());

  // <PEAK>
  Feature[] peaks = row.getPeaks();
  for (Feature p : peaks) {
    if (canceled)
      return;

    atts.clear();
    String dataFileID = dataFilesIDMap.get(p.getDataFile());
    atts.addAttribute("", "", PeakListElementName.COLUMN.getElementName(), "CDATA", dataFileID);
    atts.addAttribute("", "", PeakListElementName.MZ.getElementName(), "CDATA",
        String.valueOf(p.getMZ()));
    // In the project file, retention time is represented in seconds,
    // for historical reasons
    double rt = p.getRT() * 60d;
    atts.addAttribute("", "", PeakListElementName.RT.getElementName(), "CDATA",
        String.valueOf(rt));
    atts.addAttribute("", "", PeakListElementName.HEIGHT.getElementName(), "CDATA",
        String.valueOf(p.getHeight()));
    atts.addAttribute("", "", PeakListElementName.AREA.getElementName(), "CDATA",
        String.valueOf(p.getArea()));
    atts.addAttribute("", "", PeakListElementName.STATUS.getElementName(), "CDATA",
        p.getFeatureStatus().toString());
    atts.addAttribute("", "", PeakListElementName.CHARGE.getElementName(), "CDATA",
        String.valueOf(p.getCharge()));
    atts.addAttribute("", "", PeakListElementName.PARENT_CHROMATOGRAM_ROW_ID.getElementName(),
        "CDATA",
        p.getParentChromatogramRowID() != null ? String.valueOf(p.getParentChromatogramRowID())
            : "");
    hd.startElement("", "", PeakListElementName.PEAK.getElementName(), atts);

    fillPeakElement(p, hd);
    hd.endElement("", "", PeakListElementName.PEAK.getElementName());
  }

}

Source File: PeakListSaveHandler.java From mzmine2 with GNU General Public License v2.0

4 votes

/**
 * Add the peaks information into the XML document
 * 
 * @param peak
 * @param element
 * @param dataFileID
 * @throws IOException
 */
private void fillPeakElement(Feature peak, TransformerHandler hd)
    throws SAXException, IOException {
  AttributesImpl atts = new AttributesImpl();

  // <REPRESENTATIVE_SCAN>
  hd.startElement("", "", PeakListElementName.REPRESENTATIVE_SCAN.getElementName(), atts);
  hd.characters(String.valueOf(peak.getRepresentativeScanNumber()).toCharArray(), 0,
      String.valueOf(peak.getRepresentativeScanNumber()).length());
  hd.endElement("", "", PeakListElementName.REPRESENTATIVE_SCAN.getElementName());

  // <FRAGMENT_SCAN>
  hd.startElement("", "", PeakListElementName.FRAGMENT_SCAN.getElementName(), atts);
  hd.characters(String.valueOf(peak.getMostIntenseFragmentScanNumber()).toCharArray(), 0,
      String.valueOf(peak.getMostIntenseFragmentScanNumber()).length());
  hd.endElement("", "", PeakListElementName.FRAGMENT_SCAN.getElementName());

  // <ALL_MS2_FRAGMENT_SCANS>
  fillAllMS2FragmentScanNumbers(peak.getAllMS2FragmentScanNumbers(), hd);

  int scanNumbers[] = peak.getScanNumbers();

  // <ISOTOPE_PATTERN>
  IsotopePattern isotopePattern = peak.getIsotopePattern();
  if (isotopePattern != null) {
    atts.addAttribute("", "", PeakListElementName.STATUS.getElementName(), "CDATA",
        String.valueOf(isotopePattern.getStatus()));
    atts.addAttribute("", "", PeakListElementName.DESCRIPTION.getElementName(), "CDATA",
        isotopePattern.getDescription());
    hd.startElement("", "", PeakListElementName.ISOTOPE_PATTERN.getElementName(), atts);
    atts.clear();

    fillIsotopePatternElement(isotopePattern, hd);

    hd.endElement("", "", PeakListElementName.ISOTOPE_PATTERN.getElementName());

  }

  // <MZPEAK>
  atts.addAttribute("", "", PeakListElementName.QUANTITY.getElementName(), "CDATA",
      String.valueOf(scanNumbers.length));
  hd.startElement("", "", PeakListElementName.MZPEAKS.getElementName(), atts);
  atts.clear();

  // <SCAN_ID> <MASS> <HEIGHT>
  ByteArrayOutputStream byteScanStream = new ByteArrayOutputStream();
  DataOutputStream dataScanStream = new DataOutputStream(byteScanStream);

  ByteArrayOutputStream byteMassStream = new ByteArrayOutputStream();
  DataOutputStream dataMassStream = new DataOutputStream(byteMassStream);

  ByteArrayOutputStream byteHeightStream = new ByteArrayOutputStream();
  DataOutputStream dataHeightStream = new DataOutputStream(byteHeightStream);

  float mass, height;
  for (int scan : scanNumbers) {
    dataScanStream.writeInt(scan);
    dataScanStream.flush();
    DataPoint mzPeak = peak.getDataPoint(scan);
    if (mzPeak != null) {
      mass = (float) mzPeak.getMZ();
      height = (float) mzPeak.getIntensity();
    } else {
      mass = 0f;
      height = 0f;
    }
    dataMassStream.writeFloat(mass);
    dataMassStream.flush();
    dataHeightStream.writeFloat(height);
    dataHeightStream.flush();
  }

  byte[] bytes = Base64.encode(byteScanStream.toByteArray());
  hd.startElement("", "", PeakListElementName.SCAN_ID.getElementName(), atts);
  String sbytes = new String(bytes);
  hd.characters(sbytes.toCharArray(), 0, sbytes.length());
  hd.endElement("", "", PeakListElementName.SCAN_ID.getElementName());

  bytes = Base64.encode(byteMassStream.toByteArray());
  hd.startElement("", "", PeakListElementName.MZ.getElementName(), atts);
  sbytes = new String(bytes);
  hd.characters(sbytes.toCharArray(), 0, sbytes.length());
  hd.endElement("", "", PeakListElementName.MZ.getElementName());

  bytes = Base64.encode(byteHeightStream.toByteArray());
  hd.startElement("", "", PeakListElementName.HEIGHT.getElementName(), atts);
  sbytes = new String(bytes);
  hd.characters(sbytes.toCharArray(), 0, sbytes.length());
  hd.endElement("", "", PeakListElementName.HEIGHT.getElementName());

  hd.endElement("", "", PeakListElementName.MZPEAKS.getElementName());
}

Source File: UserParameterSaveHandler.java From mzmine3 with GNU General Public License v2.0

2 votes

/**
 * Function which creates an XML file with user parameters
 */
void saveParameters() throws SAXException, IOException, TransformerConfigurationException {

  logger.info("Saving user parameters");

  StreamResult streamResult = new StreamResult(finalStream);
  SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance();

  TransformerHandler hd = tf.newTransformerHandler();

  Transformer serializer = hd.getTransformer();
  serializer.setOutputProperty(OutputKeys.INDENT, "yes");
  serializer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");

  hd.setResult(streamResult);
  hd.startDocument();

  UserParameter<?, ?> projectParameters[] = project.getParameters();

  AttributesImpl atts = new AttributesImpl();

  atts.addAttribute("", "", UserParameterElementName.COUNT.getElementName(), "CDATA",
      String.valueOf(projectParameters.length));

  hd.startElement("", "", UserParameterElementName.PARAMETERS.getElementName(), atts);

  atts.clear();

  // <PARAMETER>
  for (UserParameter<?, ?> parameter : project.getParameters()) {

    if (canceled)
      return;

    logger.finest("Saving user parameter " + parameter.getName());

    atts.addAttribute("", "", UserParameterElementName.NAME.getElementName(), "CDATA",
        parameter.getName());

    atts.addAttribute("", "", UserParameterElementName.TYPE.getElementName(), "CDATA",
        parameter.getClass().getSimpleName());

    hd.startElement("", "", UserParameterElementName.PARAMETER.getElementName(), atts);

    atts.clear();

    fillParameterElement(parameter, hd);

    hd.endElement("", "", UserParameterElementName.PARAMETER.getElementName());
    completedParameters++;
  }

  hd.endElement("", "", UserParameterElementName.PARAMETERS.getElementName());

  hd.endDocument();

}

Source File: UserParameterSaveHandler.java From mzmine3 with GNU General Public License v2.0

2 votes

/**
 * Create the part of the XML document related to the scans
 *
 * @param scan
 * @param element
 */
private void fillParameterElement(UserParameter<?, ?> parameter, TransformerHandler hd)
    throws SAXException, IOException {

  AttributesImpl atts = new AttributesImpl();

  RawDataFile dataFiles[] = project.getDataFiles();

  if (parameter instanceof ComboParameter) {
    Object choices[] = ((ComboParameter<?>) parameter).getChoices().toArray();

    for (Object choice : choices) {
      hd.startElement("", "", UserParameterElementName.OPTION.getElementName(), atts);

      hd.characters(choice.toString().toCharArray(), 0, choice.toString().length());
      hd.endElement("", "", UserParameterElementName.OPTION.getElementName());
    }

  }

  for (RawDataFile dataFile : dataFiles) {

    Object value = project.getParameterValue(parameter, dataFile);

    if (value == null)
      continue;

    String valueString = String.valueOf(value);
    String dataFileID = dataFilesIDMap.get(dataFile);

    atts.addAttribute("", "", UserParameterElementName.DATA_FILE.getElementName(), "CDATA",
        dataFileID);

    hd.startElement("", "", UserParameterElementName.VALUE.getElementName(), atts);

    atts.clear();

    hd.characters(valueString.toCharArray(), 0, valueString.length());
    hd.endElement("", "", UserParameterElementName.VALUE.getElementName());

  }

}

Source File: UserParameterSaveHandler.java From mzmine2 with GNU General Public License v2.0

2 votes

/**
 * Function which creates an XML file with user parameters
 */
void saveParameters() throws SAXException, IOException, TransformerConfigurationException {

  logger.info("Saving user parameters");

  StreamResult streamResult = new StreamResult(finalStream);
  SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance();

  TransformerHandler hd = tf.newTransformerHandler();

  Transformer serializer = hd.getTransformer();
  serializer.setOutputProperty(OutputKeys.INDENT, "yes");
  serializer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");

  hd.setResult(streamResult);
  hd.startDocument();

  UserParameter<?, ?> projectParameters[] = project.getParameters();

  AttributesImpl atts = new AttributesImpl();

  atts.addAttribute("", "", UserParameterElementName.COUNT.getElementName(), "CDATA",
      String.valueOf(projectParameters.length));

  hd.startElement("", "", UserParameterElementName.PARAMETERS.getElementName(), atts);

  atts.clear();

  // <PARAMETER>
  for (UserParameter<?, ?> parameter : project.getParameters()) {

    if (canceled)
      return;

    logger.finest("Saving user parameter " + parameter.getName());

    atts.addAttribute("", "", UserParameterElementName.NAME.getElementName(), "CDATA",
        parameter.getName());

    atts.addAttribute("", "", UserParameterElementName.TYPE.getElementName(), "CDATA",
        parameter.getClass().getSimpleName());

    hd.startElement("", "", UserParameterElementName.PARAMETER.getElementName(), atts);

    atts.clear();

    fillParameterElement(parameter, hd);

    hd.endElement("", "", UserParameterElementName.PARAMETER.getElementName());
    completedParameters++;
  }

  hd.endElement("", "", UserParameterElementName.PARAMETERS.getElementName());

  hd.endDocument();

}

Java Code Examples for javax.xml.transform.sax.TransformerHandler#endElement()