Java Code Examples for org.xml.sax.helpers.AttributesImpl#clear()
The following examples show how to use
org.xml.sax.helpers.AttributesImpl#clear() .
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Example 1
| 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());
}
}
Example 2
| 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 3
| Source File: CanonicalXTMWriter.java From ontopia with Apache License 2.0 | 6 votes |
|
private void write(TopicNameIF basename, int number) {
AttributesImpl attributes = reifier(basename);
attributes.addAttribute("", "", AT_NUMBER, null, "" + number);
startElement(EL_NAME, attributes);
attributes.clear();
write(basename.getValue());
writeType(basename);
write(basename.getScope());
Object[] variants = basename.getVariants().toArray();
Arrays.sort(variants, variantComparator);
for (int ix = 0; ix < variants.length; ix++)
write((VariantNameIF) variants[ix], ix + 1);
writeLocators(basename.getItemIdentifiers(), EL_ITEMIDENTIFIERS);
endElement(EL_NAME);
}
Example 4
| Source File: RelationMapping.java From ontopia with Apache License 2.0 | 5 votes |
|
protected void outputEntities(Relation rel, ContentHandler dh) throws SAXException {
AttributesImpl atts = new AttributesImpl();
for (Entity entity : rel.getEntities()) {
if (entity.getEntityType() == Entity.TYPE_TOPIC) {
// <topic>
if (entity.getId() != null)
addAttribute(atts, "id", "CDATA", entity.getId());
addAttribute(atts, "type", "CDATA", entity.getAssociationType());
dh.startElement("", "", "topic", atts);
atts.clear();
outputFields(entity, dh);
// </topic>
dh.endElement("", "", "topic");
} else if (entity.getEntityType() == Entity.TYPE_ASSOCIATION) {
// <association>
if (entity.getId() != null)
addAttribute(atts, "id", "CDATA", entity.getId());
addAttribute(atts, "type", "CDATA", entity.getAssociationType());
addAttribute(atts, "scope", "CDATA", entity.getScope());
dh.startElement("", "", "association", atts);
atts.clear();
outputFields(entity, dh);
// </association>
dh.endElement("", "", "association");
}
}
}
Example 5
| Source File: UserReportlet.java From syncope with Apache License 2.0 | 5 votes |
|
private void doExtractConf(final ContentHandler handler) throws SAXException {
AttributesImpl atts = new AttributesImpl();
handler.startElement("", "", "configurations", null);
handler.startElement("", "", "userAttributes", atts);
for (Feature feature : conf.getFeatures()) {
atts.clear();
handler.startElement("", "", "feature", atts);
handler.characters(feature.name().toCharArray(), 0, feature.name().length());
handler.endElement("", "", "feature");
}
for (String attr : conf.getPlainAttrs()) {
atts.clear();
handler.startElement("", "", "attribute", atts);
handler.characters(attr.toCharArray(), 0, attr.length());
handler.endElement("", "", "attribute");
}
for (String derAttr : conf.getDerAttrs()) {
atts.clear();
handler.startElement("", "", "derAttribute", atts);
handler.characters(derAttr.toCharArray(), 0, derAttr.length());
handler.endElement("", "", "derAttribute");
}
for (String virAttr : conf.getVirAttrs()) {
atts.clear();
handler.startElement("", "", "virAttribute", atts);
handler.characters(virAttr.toCharArray(), 0, virAttr.length());
handler.endElement("", "", "virAttribute");
}
handler.endElement("", "", "userAttributes");
handler.endElement("", "", "configurations");
}
Example 6
| Source File: CanonicalTopicMapWriter.java From ontopia with Apache License 2.0 | 5 votes |
|
/**
* PUBLIC: Exports the topic map to the given ContentHandler.
*/
public void export(TopicMapIF topicmap, ContentHandler dh)
throws IOException, SAXException {
dh.startDocument();
AttributesImpl atts = new AttributesImpl();
atts.addAttribute("", "", "xmlns", CDATA,
"http://www.topicmaps.org/cxtm/1.0/");
dh.startElement("", "", "topicMap", atts);
atts.clear();
// topics
ContextHolder context = createContext(topicmap);
Iterator<TopicIF> it = context.topicsInOrder(topicmap.getTopics());
while (it.hasNext())
writeTopic(it.next(), dh, context);
// associations
Iterator<AssociationIF> ait = context.assocsInOrder(topicmap.getAssociations());
while (ait.hasNext())
writeAssociation(ait.next(), dh, context);
dh.endElement("", "", "topicMap");
dh.endDocument();
}
Example 7
| Source File: EDIReader.java From edireader with GNU General Public License v3.0 | 5 votes |
|
protected void startXMLDocument() throws SAXException {
AttributesImpl attrList = new AttributesImpl();
attrList.clear();
final ContentHandler contentHandler = getContentHandler();
if (contentHandler == null) {
throw new SAXException("No ContentHandler configured for EDIReader");
}
contentHandler.startDocument();
String rootTag = getXMLTags().getRootTag();
if (isNamespaceEnabled()) {
contentHandler.startElement(BERRYWORKS_NAMESPACE, rootTag, rootTag, attrList);
} else {
startElement(rootTag, attrList);
}
}
Example 8
| Source File: StAX2SAXReader.java From TencentKona-8 with GNU General Public License v2.0 | 4 votes |
|
public void adapt() throws XMLStreamException, SAXException {
QName qname;
String prefix, localPart;
AttributesImpl attrs = new AttributesImpl();
char[] buffer;
int nsc;
int nat;
_handler.startDocument();
try {
while (_reader.hasNext()) {
int event = _reader.next();
switch(event) {
case XMLStreamConstants.START_ELEMENT: {
// Report namespace events first
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.startPrefixMapping(_reader.getNamespacePrefix(i),
_reader.getNamespaceURI(i));
}
// Collect list of attributes
attrs.clear();
nat = _reader.getAttributeCount();
for (int i = 0; i < nat; i++) {
QName q = _reader.getAttributeName(i);
String qName = _reader.getAttributePrefix(i);
if (qName == null || qName == "") {
qName = q.getLocalPart();
} else {
qName = qName + ":" + q.getLocalPart();
}
attrs.addAttribute(_reader.getAttributeNamespace(i),
q.getLocalPart(),
qName,
_reader.getAttributeType(i),
_reader.getAttributeValue(i));
}
// Report start element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.startElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart,
attrs);
break;
}
case XMLStreamConstants.END_ELEMENT: {
// Report end element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.endElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart);
// Report end namespace events
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.endPrefixMapping(_reader.getNamespacePrefix(i));
}
break;
}
case XMLStreamConstants.CHARACTERS:
_handler.characters(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.COMMENT:
_lexicalHandler.comment(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.PROCESSING_INSTRUCTION:
_handler.processingInstruction(_reader.getPITarget(), _reader.getPIData());
break;
case XMLStreamConstants.END_DOCUMENT:
break;
default:
throw new RuntimeException(CommonResourceBundle.getInstance().getString("message.StAX2SAXReader", new Object[]{Integer.valueOf(event)}));
} // switch
}
}
catch (XMLStreamException e) {
_handler.endDocument(); // flush whatever we have
throw e;
}
_handler.endDocument();
}
Example 9
| Source File: StAX2SAXReader.java From openjdk-jdk8u with GNU General Public License v2.0 | 4 votes |
|
public void adapt() throws XMLStreamException, SAXException {
QName qname;
String prefix, localPart;
AttributesImpl attrs = new AttributesImpl();
char[] buffer;
int nsc;
int nat;
_handler.startDocument();
try {
while (_reader.hasNext()) {
int event = _reader.next();
switch(event) {
case XMLStreamConstants.START_ELEMENT: {
// Report namespace events first
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.startPrefixMapping(_reader.getNamespacePrefix(i),
_reader.getNamespaceURI(i));
}
// Collect list of attributes
attrs.clear();
nat = _reader.getAttributeCount();
for (int i = 0; i < nat; i++) {
QName q = _reader.getAttributeName(i);
String qName = _reader.getAttributePrefix(i);
if (qName == null || qName == "") {
qName = q.getLocalPart();
} else {
qName = qName + ":" + q.getLocalPart();
}
attrs.addAttribute(_reader.getAttributeNamespace(i),
q.getLocalPart(),
qName,
_reader.getAttributeType(i),
_reader.getAttributeValue(i));
}
// Report start element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.startElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart,
attrs);
break;
}
case XMLStreamConstants.END_ELEMENT: {
// Report end element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.endElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart);
// Report end namespace events
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.endPrefixMapping(_reader.getNamespacePrefix(i));
}
break;
}
case XMLStreamConstants.CHARACTERS:
_handler.characters(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.COMMENT:
_lexicalHandler.comment(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.PROCESSING_INSTRUCTION:
_handler.processingInstruction(_reader.getPITarget(), _reader.getPIData());
break;
case XMLStreamConstants.END_DOCUMENT:
break;
default:
throw new RuntimeException(CommonResourceBundle.getInstance().getString("message.StAX2SAXReader", new Object[]{Integer.valueOf(event)}));
} // switch
}
}
catch (XMLStreamException e) {
_handler.endDocument(); // flush whatever we have
throw e;
}
_handler.endDocument();
}
Example 10
| Source File: StAX2SAXReader.java From openjdk-jdk9 with GNU General Public License v2.0 | 4 votes |
|
public void adapt() throws XMLStreamException, SAXException {
QName qname;
String prefix, localPart;
AttributesImpl attrs = new AttributesImpl();
char[] buffer;
int nsc;
int nat;
_handler.startDocument();
try {
while (_reader.hasNext()) {
int event = _reader.next();
switch(event) {
case XMLStreamConstants.START_ELEMENT: {
// Report namespace events first
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.startPrefixMapping(_reader.getNamespacePrefix(i),
_reader.getNamespaceURI(i));
}
// Collect list of attributes
attrs.clear();
nat = _reader.getAttributeCount();
for (int i = 0; i < nat; i++) {
QName q = _reader.getAttributeName(i);
String qName = _reader.getAttributePrefix(i);
if (qName == null || qName == "") {
qName = q.getLocalPart();
} else {
qName = qName + ":" + q.getLocalPart();
}
attrs.addAttribute(_reader.getAttributeNamespace(i),
q.getLocalPart(),
qName,
_reader.getAttributeType(i),
_reader.getAttributeValue(i));
}
// Report start element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.startElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart,
attrs);
break;
}
case XMLStreamConstants.END_ELEMENT: {
// Report end element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.endElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart);
// Report end namespace events
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.endPrefixMapping(_reader.getNamespacePrefix(i));
}
break;
}
case XMLStreamConstants.CHARACTERS:
_handler.characters(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.COMMENT:
_lexicalHandler.comment(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.PROCESSING_INSTRUCTION:
_handler.processingInstruction(_reader.getPITarget(), _reader.getPIData());
break;
case XMLStreamConstants.END_DOCUMENT:
break;
default:
throw new RuntimeException(CommonResourceBundle.getInstance().getString("message.StAX2SAXReader", new Object[]{Integer.valueOf(event)}));
} // switch
}
}
catch (XMLStreamException e) {
_handler.endDocument(); // flush whatever we have
throw e;
}
_handler.endDocument();
}
Example 11
| 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 12
| Source File: StAX2SAXReader.java From openjdk-8-source with GNU General Public License v2.0 | 4 votes |
|
public void adapt() throws XMLStreamException, SAXException {
QName qname;
String prefix, localPart;
AttributesImpl attrs = new AttributesImpl();
char[] buffer;
int nsc;
int nat;
_handler.startDocument();
try {
while (_reader.hasNext()) {
int event = _reader.next();
switch(event) {
case XMLStreamConstants.START_ELEMENT: {
// Report namespace events first
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.startPrefixMapping(_reader.getNamespacePrefix(i),
_reader.getNamespaceURI(i));
}
// Collect list of attributes
attrs.clear();
nat = _reader.getAttributeCount();
for (int i = 0; i < nat; i++) {
QName q = _reader.getAttributeName(i);
String qName = _reader.getAttributePrefix(i);
if (qName == null || qName == "") {
qName = q.getLocalPart();
} else {
qName = qName + ":" + q.getLocalPart();
}
attrs.addAttribute(_reader.getAttributeNamespace(i),
q.getLocalPart(),
qName,
_reader.getAttributeType(i),
_reader.getAttributeValue(i));
}
// Report start element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.startElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart,
attrs);
break;
}
case XMLStreamConstants.END_ELEMENT: {
// Report end element
qname = _reader.getName();
prefix = qname.getPrefix();
localPart = qname.getLocalPart();
_handler.endElement(_reader.getNamespaceURI(),
localPart,
(prefix.length() > 0) ?
(prefix + ":" + localPart) : localPart);
// Report end namespace events
nsc = _reader.getNamespaceCount();
for (int i = 0; i < nsc; i++) {
_handler.endPrefixMapping(_reader.getNamespacePrefix(i));
}
break;
}
case XMLStreamConstants.CHARACTERS:
_handler.characters(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.COMMENT:
_lexicalHandler.comment(_reader.getTextCharacters(), _reader.getTextStart(), _reader.getTextLength());
break;
case XMLStreamConstants.PROCESSING_INSTRUCTION:
_handler.processingInstruction(_reader.getPITarget(), _reader.getPIData());
break;
case XMLStreamConstants.END_DOCUMENT:
break;
default:
throw new RuntimeException(CommonResourceBundle.getInstance().getString("message.StAX2SAXReader", new Object[]{Integer.valueOf(event)}));
} // switch
}
}
catch (XMLStreamException e) {
_handler.endDocument(); // flush whatever we have
throw e;
}
_handler.endDocument();
}
Example 13
| Source File: SaverBase.java From ganttproject with GNU General Public License v3.0 | 4 votes |
|
protected void emptyElement(String name, AttributesImpl attrs, TransformerHandler handler) throws SAXException {
startElement(name, attrs, handler);
endElement(name, handler);
attrs.clear();
}
Example 14
| 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 15
| Source File: SAXDecoder.java From exificient with MIT License | 4 votes |
|
protected void handleDeferredStartElement(EXIBodyDecoder decoder,
QNameContext deferredStartElement, final AttributesImpl attributes)
throws SAXException, IOException, EXIException {
if (namespaces) {
List<NamespaceDeclaration> prefixes = decoder
.getDeclaredPrefixDeclarations();
if (prefixes != null) {
for (int i = 0; i < prefixes.size(); i++) {
NamespaceDeclaration ns = prefixes.get(i);
contentHandler.startPrefixMapping(ns.prefix,
ns.namespaceURI);
}
}
}
/*
* the qualified name is required when the namespace-prefixes property
* is true, and is optional when the namespace-prefixes property is
* false (the default).
*/
// String seQNameAsString = Constants.EMPTY_STRING;
// if (namespacePrefixes) {
// seQNameAsString = decoder.getElementQNameAsString();
// }
/*
* Note: it looks like widely used APIs (Xerces, Saxon, ..) provide the
* textual qname even when
* http://xml.org/sax/features/namespace-prefixes is set to false
* http:// sourceforge.net/projects/exificient/forums/forum/856596/topic
* /5839494
*/
String seQNameAsString = decoder.getElementQNameAsString();
// start so far deferred start element
contentHandler.startElement(deferredStartElement.getNamespaceUri(),
deferredStartElement.getLocalName(), seQNameAsString,
attributes);
// clear AT information
attributes.clear();
}
Example 16
| 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 17
| Source File: GroupReportlet.java From syncope with Apache License 2.0 | 4 votes |
|
private void doExtract(final ContentHandler handler, final List<Group> groups) throws SAXException {
AttributesImpl atts = new AttributesImpl();
for (Group group : groups) {
atts.clear();
for (Feature feature : conf.getFeatures()) {
String type = null;
String value = null;
switch (feature) {
case key:
type = ReportXMLConst.XSD_STRING;
value = group.getKey();
break;
case name:
type = ReportXMLConst.XSD_STRING;
value = String.valueOf(group.getName());
break;
case groupOwner:
type = ReportXMLConst.XSD_STRING;
value = group.getGroupOwner().getKey();
break;
case userOwner:
type = ReportXMLConst.XSD_STRING;
value = group.getUserOwner().getKey();
break;
default:
}
if (type != null && value != null) {
atts.addAttribute("", "", feature.name(), type, value);
}
}
handler.startElement("", "", "group", atts);
// Using GroupTO for attribute values, since the conversion logic of
// values to String is already encapsulated there
GroupTO groupTO = groupDataBinder.getGroupTO(group, true);
doExtractAttributes(handler, groupTO, conf.getPlainAttrs(), conf.getDerAttrs(), conf.getVirAttrs());
// to get resources associated to a group
if (conf.getFeatures().contains(Feature.resources)) {
doExtractResources(handler, groupTO);
}
//to get users asscoiated to a group is preferred GroupDAO to GroupTO
if (conf.getFeatures().contains(Feature.users)) {
handler.startElement("", "", "users", null);
for (UMembership memb : groupDAO.findUMemberships(group)) {
atts.clear();
atts.addAttribute("", "", "key", ReportXMLConst.XSD_STRING,
memb.getLeftEnd().getKey());
atts.addAttribute("", "", "username", ReportXMLConst.XSD_STRING,
String.valueOf(memb.getLeftEnd().getUsername()));
handler.startElement("", "", "user", atts);
handler.endElement("", "", "user");
}
handler.endElement("", "", "users");
}
handler.endElement("", "", "group");
}
}
Example 18
| 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 19
| 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 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());
}
}
