Java Code Examples for javax.xml.transform.sax.TransformerHandler#startElement()
The following examples show how to use
javax.xml.transform.sax.TransformerHandler#startElement() .
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Example 1
| Source File: IvyArtifactReport.java From ant-ivy with Apache License 2.0 | 6 votes |
|
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");
}
}
Example 2
| Source File: PeakListSaveHandler.java From mzmine3 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());
}
}
Example 3
| 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());
}
}
Example 4
| 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());
}
}
Example 5
| Source File: IvyArtifactReport.java From ant-ivy with Apache License 2.0 | 5 votes |
|
private void startModule(TransformerHandler saxHandler, IvyNode dependency) throws SAXException {
AttributesImpl moduleAttrs = new AttributesImpl();
moduleAttrs.addAttribute(null, "organisation", "organisation", "CDATA", dependency
.getModuleId().getOrganisation());
moduleAttrs.addAttribute(null, "name", "name", "CDATA", dependency.getModuleId().getName());
ResolvedModuleRevision moduleRevision = dependency.getModuleRevision();
moduleAttrs.addAttribute(null, "rev", "rev", "CDATA", moduleRevision.getId().getRevision());
moduleAttrs.addAttribute(null, "status", "status", "CDATA", moduleRevision.getDescriptor()
.getStatus());
saxHandler.startElement(null, "module", "module", moduleAttrs);
}
Example 6
| 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());
}
}
}
Example 7
| Source File: PeakListSaveHandler.java From mzmine2 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());
}
}
Example 8
| Source File: IvyArtifactReport.java From ant-ivy with Apache License 2.0 | 5 votes |
|
private void startArtifact(TransformerHandler saxHandler, Artifact artifact)
throws SAXException {
AttributesImpl artifactAttrs = new AttributesImpl();
artifactAttrs.addAttribute(null, "name", "name", "CDATA", artifact.getName());
artifactAttrs.addAttribute(null, "ext", "ext", "CDATA", artifact.getExt());
artifactAttrs.addAttribute(null, "type", "type", "CDATA", artifact.getType());
saxHandler.startElement(null, "artifact", "artifact", artifactAttrs);
}
Example 9
| 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) {
}
}
Example 10
| 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());
}
}
Example 11
| 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());
}
}
Example 12
| Source File: IvyArtifactReport.java From ant-ivy with Apache License 2.0 | 4 votes |
|
private void generateXml(IvyNode[] dependencies,
Map<ModuleRevisionId, Set<ArtifactDownloadReport>> moduleRevToArtifactsMap,
Map<ArtifactDownloadReport, Set<String>> artifactsToCopy) {
try {
try (FileOutputStream fileOutputStream = new FileOutputStream(tofile)) {
TransformerHandler saxHandler = createTransformerHandler(fileOutputStream);
saxHandler.startDocument();
saxHandler.startElement(null, "modules", "modules", new AttributesImpl());
for (IvyNode dependency : dependencies) {
if (dependency.getModuleRevision() == null
|| dependency.isCompletelyEvicted()) {
continue;
}
startModule(saxHandler, dependency);
Set<ArtifactDownloadReport> artifactsOfModuleRev = moduleRevToArtifactsMap.get(dependency
.getModuleRevision().getId());
if (artifactsOfModuleRev != null) {
for (ArtifactDownloadReport artifact : artifactsOfModuleRev) {
RepositoryCacheManager cache = dependency.getModuleRevision()
.getArtifactResolver().getRepositoryCacheManager();
startArtifact(saxHandler, artifact.getArtifact());
writeOriginLocationIfPresent(cache, saxHandler, artifact);
writeCacheLocationIfPresent(cache, saxHandler, artifact);
for (String artifactDestPath : artifactsToCopy.get(artifact)) {
writeRetrieveLocation(saxHandler, artifactDestPath);
}
saxHandler.endElement(null, "artifact", "artifact");
}
}
saxHandler.endElement(null, "module", "module");
}
saxHandler.endElement(null, "modules", "modules");
saxHandler.endDocument();
}
} catch (SAXException | IOException | TransformerConfigurationException e) {
throw new BuildException("impossible to generate report", e);
}
}
Example 13
| 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());
}
Example 14
| Source File: XmlWriter.java From CloverETL-Engine with GNU Lesser General Public License v2.1 | 4 votes |
|
/**
* Creates output XML from all read records using SAX.
* Call this after all records are stored in PortDefinition structures.
* @throws TransformerConfigurationException
* @throws SAXException
* @throws IOException
*/
/*
private void flushXmlSax() throws TransformerConfigurationException, SAXException, IOException {
FileOutputStream fos = new FileOutputStream(fileUrl);
TransformerHandler hd = createHeader(fos);
PortDefinition portDefinition = rootPortDefinition;
// for each record of port
for (Map.Entry<HashKey, TreeRecord> e : portDefinition.dataMap.entrySet()){
TreeRecord record = e.getValue();
List<DataRecord> records = new ArrayList<DataRecord>();
records.add(record.record);
addRecords(hd, records, portDefinition);
}// for record
createFooter(fos, hd);
}*/
private TransformerHandler createHeader(OutputStream os) throws FileNotFoundException, TransformerConfigurationException, SAXException {
StreamResult streamResult = new StreamResult(os);
SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance();
// SAX2.0 ContentHandler.
TransformerHandler hd = tf.newTransformerHandler();
Transformer serializer = hd.getTransformer();
serializer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
serializer.setOutputProperty(OutputKeys.ENCODING, this.charset);
//serializer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM,"users.dtd");
if (omitNewLines)
serializer.setOutputProperty(OutputKeys.INDENT,"no");
else
serializer.setOutputProperty(OutputKeys.INDENT,"yes");
hd.setResult(streamResult);
hd.startDocument();
String root = (rootElement!=null && rootElement.length()>0) ? rootElement : DEFAULT_ROOT_ELEMENT;
if (useRootElement && dtdPublicId != null && dtdPublicId.trim().length()>0 && dtdSystemId != null && dtdSystemId.trim().length()>0){
hd.startDTD(root, dtdPublicId, dtdSystemId);
hd.endDTD();
}
//if (recordsPerFile!=1){
if (this.useRootElement) {
AttributesImpl atts = new AttributesImpl();
if (rootInfoAttributes) {
atts.addAttribute("", ATTRIBUTE_COMPONENT_ID, ATTRIBUTE_COMPONENT_ID, "CDATA", getId());
atts.addAttribute("", ATTRIBUTE_GRAPH_NAME, ATTRIBUTE_GRAPH_NAME, "CDATA", this.getGraph().getName());
atts.addAttribute("", ATTRIBUTE_CREATED, ATTRIBUTE_CREATED, "CDATA", (new Date()).toString());
}
if (!StringUtils.isEmpty(xsdSchemaLocation)) {
atts.addAttribute(XSI_URI, "schemaLocation", "xsi:schemaLocation", "CDATA", this.xsdSchemaLocation);
}
for (String prefix : namespaces.keySet()) {
String uri = namespaces.get(prefix);
hd.startPrefixMapping(prefix, uri);
}
if (!rootDefaultNamespace.isEmpty()) {
hd.startPrefixMapping("", rootDefaultNamespace);
}
hd.startElement(rootDefaultNamespace, getLocalName(root), root, atts);
}
return hd;
}
Example 15
| 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());
}
Example 16
| Source File: SaverBase.java From ganttproject with GNU General Public License v3.0 | 4 votes |
|
protected void startElement(String name, AttributesImpl attrs, TransformerHandler handler) throws SAXException {
handler.startElement("", name, name, attrs);
attrs.clear();
}
Example 17
| 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());
}
}
Example 18
| 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();
}
Example 19
| 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();
}
Example 20
| Source File: UserParameterSaveHandler.java From mzmine2 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();
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());
}
}
