下面列出了javax.xml.transform.sax.TransformerHandler#characters ( ) 实例代码,或者点击链接到github查看源代码,也可以在右侧发表评论。
/**
* 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());
}
}
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());
}
}
@Test
public final void testXMLStackOverflowBug() throws TransformerConfigurationException, IOException, SAXException {
try {
SAXTransformerFactory stf = (SAXTransformerFactory) TransformerFactory.newInstance();
TransformerHandler ser = stf.newTransformerHandler();
ser.setResult(new StreamResult(System.out));
StringBuilder sb = new StringBuilder(4096);
for (int x = 4096; x > 0; x--) {
sb.append((char) x);
}
ser.characters(sb.toString().toCharArray(), 0, sb.toString().toCharArray().length);
ser.endDocument();
} catch (StackOverflowError se) {
se.printStackTrace();
Assert.fail("StackOverflow");
}
}
@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());
}
/**
* 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());
}
}
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());
}
}
private void writeOriginLocationIfPresent(RepositoryCacheManager cache,
TransformerHandler saxHandler, ArtifactDownloadReport artifact) throws SAXException {
ArtifactOrigin origin = artifact.getArtifactOrigin();
if (!ArtifactOrigin.isUnknown(origin)) {
String originName = origin.getLocation();
boolean isOriginLocal = origin.isLocal();
String originLocation;
AttributesImpl originLocationAttrs = new AttributesImpl();
if (isOriginLocal) {
originLocationAttrs.addAttribute(null, "is-local", "is-local", "CDATA", "true");
originLocation = originName.replace('\\', '/');
} else {
originLocationAttrs.addAttribute(null, "is-local", "is-local", "CDATA", "false");
originLocation = originName;
}
saxHandler
.startElement(null, "origin-location", "origin-location", originLocationAttrs);
char[] originLocationAsChars = originLocation.toCharArray();
saxHandler.characters(originLocationAsChars, 0, originLocationAsChars.length);
saxHandler.endElement(null, "origin-location", "origin-location");
}
}
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());
}
}
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());
}
}
}
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());
}
}
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());
}
}
}
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");
}
protected void cdataElement(String name, String cdata, AttributesImpl attrs, TransformerHandler handler)
throws SAXException {
if (cdata == null) {
return;
}
startElement(name, attrs, handler);
handler.startCDATA();
handler.characters(cdata.toCharArray(), 0, cdata.length());
handler.endCDATA();
endElement(name, handler);
}
protected void textElement(String name, AttributesImpl attrs, String text, TransformerHandler handler)
throws SAXException {
if (text != null) {
startElement(name, attrs, handler);
handler.startCDATA();
handler.characters(text.toCharArray(), 0, text.length());
handler.endCDATA();
endElement(name, handler);
attrs.clear();
}
}
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");
}
}
/**
* 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());
}
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) {
}
}
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();
}
}
/**
* 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());
}
/**
* 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());
}
}