private static void toXml(XmlWriter w, Resource resource) throws IOException {
w.element(RepositoryParser.RESOURCE)
.attribute(Resource.ID, resource.getId())
.attribute(Resource.SYMBOLIC_NAME, resource.getSymbolicName())
.attribute(Resource.PRESENTATION_NAME, resource.getPresentationName())
.attribute(Resource.URI, getRelativeUri(resource, Resource.URI))
.attribute(Resource.VERSION, resource.getVersion().toString());
w.textElement(Resource.DESCRIPTION, resource.getProperties().get(Resource.DESCRIPTION))
.textElement(Resource.SIZE, resource.getProperties().get(Resource.SIZE))
.textElement(
Resource.DOCUMENTATION_URI, getRelativeUri(resource, Resource.DOCUMENTATION_URI))
.textElement(Resource.SOURCE_URI, getRelativeUri(resource, Resource.SOURCE_URI))
.textElement(Resource.JAVADOC_URI, getRelativeUri(resource, Resource.JAVADOC_URI))
.textElement(Resource.LICENSE_URI, getRelativeUri(resource, Resource.LICENSE_URI));
String[] categories = resource.getCategories();
for (int i = 0; categories != null && i < categories.length; i++) {
w.element(RepositoryParser.CATEGORY).attribute(RepositoryParser.ID, categories[i]).end();
}
Capability[] capabilities = resource.getCapabilities();
for (int i = 0; capabilities != null && i < capabilities.length; i++) {
toXml(w, capabilities[i]);
}
Requirement[] requirements = resource.getRequirements();
for (int i = 0; requirements != null && i < requirements.length; i++) {
toXml(w, requirements[i]);
}
w.end();
}
public static Element ranking_Genes(Document doc, IndividualStat is, int number) {
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
float[] scores = null;
Integer[] index;
if (number > Symbols.length) number = Symbols.length;
if (is != null) {
index = is.get_Order();
scores = is.get_GeneScores(Symbols.length - 1, 0);
for (int i = Symbols.length - 1; i >= Symbols.length - number; i--) {
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols[index[i]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_CHROMOSOME, ChrList[Chrs[index[i]]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[index[i]] + 1));
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[index[i]]));
XmlWriter.append_text_element(
doc,
gene,
Consts.XML_TAG_SCORE,
Float.toString(Math.round(scores[index[i]] * 10) / 10));
genes.appendChild(gene);
}
}
return genes;
}
public static Element overlap_Genes(
Document doc, String chr, int start, int end, IndividualStat is) {
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
if (ChrMap.containsKey(chr)) {
int[] range = binarySearchOverlap(ChrMap.get(chr), start, end);
if (range != null) {
float[] scores = null;
if (is != null) scores = is.get_GeneScores(range[1], range[0]);
for (int i = range[0]; i <= range[1]; i++) {
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols[i]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[i] + 1));
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[i]));
if (is != null)
XmlWriter.append_text_element(
doc,
gene,
Consts.XML_TAG_SCORE,
Float.toString(Math.round(scores[i - range[0]] * 10) / 10));
genes.appendChild(gene);
}
}
}
return genes;
}
public static Element find_Gene(Document doc, String prefix) {
prefix = prefix.toUpperCase();
if (prefix.matches("C[XY0-9]+ORF")) {
prefix = prefix.replaceFirst("ORF", "orf");
} else if (prefix.matches("C[XY0-9]+OR")) {
prefix = prefix.replaceFirst("OR", "or");
} else if (prefix.matches("^C[XY0-9]+O")) {
prefix = prefix.replaceFirst("O", "o");
}
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
int match = binarySearchPrefix(prefix);
if (match >= 0) {
for (int i = match; i < match + 5; i++) {
if (i >= Symbols_sorted.length || !Symbols_sorted[i].startsWith(prefix)) return genes;
else {
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols_sorted[i]);
int index = SymbolMap.get(Symbols_sorted[i]);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_CHROMOSOME, ChrList[Chrs[index]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[index] + 1));
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[index]));
genes.appendChild(gene);
}
}
}
return genes;
}
private static void toXml(XmlWriter w, Capability capability) throws IOException {
w.element(RepositoryParser.CAPABILITY).attribute(RepositoryParser.NAME, capability.getName());
Property[] props = capability.getProperties();
for (int j = 0; props != null && j < props.length; j++) {
toXml(w, props[j]);
}
w.end();
}
public static Element gene_Info(Document doc, String symbol) {
Element genes = doc.createElement(Consts.XML_TAG_GENES);
doc.getElementsByTagName(Consts.DATA_ROOT).item(0).appendChild(genes);
if (SymbolMap.containsKey(symbol)) {
int index = SymbolMap.get(symbol);
Element gene = doc.createElement(Consts.XML_TAG_GENE);
gene.setAttribute(Consts.XML_TAG_ID, Symbols[index]);
genes.appendChild(gene);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_CHROMOSOME, ChrList[Chrs[index]]);
XmlWriter.append_text_element(
doc, gene, Consts.XML_TAG_FROM, Integer.toString(Starts[index] + 1));
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_TO, Integer.toString(Ends[index]));
if (!RefSeqs[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_REFSEQ, RefSeqs[index]);
if (!UCSCs[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_UCSC, UCSCs[index]);
if (!Ensembls[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_ENSEMBL, Ensembls[index]);
if (!Entrezs[index].equals(""))
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_ENTREZ, Entrezs[index]);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_HGNC, HGNCs[index]);
XmlWriter.append_text_element(doc, gene, Consts.XML_TAG_NAME, Names[index]);
}
return genes;
}
private void serializeValue(final HttpServletResponse pResponse, Object value)
throws TransformerException, IOException, FactoryConfigurationError {
if (value instanceof Source) {
setContentType(pResponse, "application/binary"); // Unknown content type
Sources.writeToStream((Source) value, pResponse.getOutputStream());
} else if (value instanceof Node) {
pResponse.setContentType("text/xml");
Sources.writeToStream(new DOMSource((Node) value), pResponse.getOutputStream());
} else if (value instanceof XmlSerializable) {
pResponse.setContentType("text/xml");
XMLOutputFactory factory = XMLOutputFactory.newInstance();
factory.setProperty(XMLOutputFactory.IS_REPAIRING_NAMESPACES, Boolean.TRUE);
try {
XmlWriter out =
XmlStreaming.newWriter(
pResponse.getOutputStream(), pResponse.getCharacterEncoding(), true);
try {
out.startDocument(null, null, null);
((XmlSerializable) value).serialize(out);
out.endDocument();
} finally {
out.close();
}
} catch (XmlException e) {
throw new TransformerException(e);
}
} else if (value instanceof Collection) {
final XmlElementWrapper annotation = getElementWrapper();
if (annotation != null) {
setContentType(pResponse, "text/xml");
try (OutputStream outStream = pResponse.getOutputStream()) {
writeCollection(
outStream, getGenericReturnType(), (Collection<?>) value, getQName(annotation));
}
}
} else if (value instanceof CharSequence) {
setContentType(pResponse, "text/plain");
pResponse.getWriter().append((CharSequence) value);
} else {
if (value != null) {
try {
final JAXBContext jaxbContext = JAXBContext.newInstance(getReturnType());
setContentType(pResponse, "text/xml");
final JAXBSource jaxbSource = new JAXBSource(jaxbContext, value);
Sources.writeToStream(jaxbSource, pResponse.getOutputStream());
} catch (final JAXBException e) {
throw new MessagingException(e);
}
}
}
}
private static void saveUserListWithoutLock()
throws TransformerConfigurationException, SAXException, IOException, SearchLibException {
ConfigFileRotation cfr =
configFiles.get(StartStopListener.OPENSEARCHSERVER_DATA_FILE, "users.xml");
try {
XmlWriter xmlWriter = new XmlWriter(cfr.getTempPrintWriter("UTF-8"), "UTF-8");
getUserList().writeXml(xmlWriter);
xmlWriter.endDocument();
cfr.rotate();
} finally {
cfr.abort();
}
}
private static void toXml(XmlWriter w, Property property) throws IOException {
w.element(RepositoryParser.P)
.attribute(RepositoryParser.N, property.getName())
.attribute(RepositoryParser.T, property.getType())
.attribute(RepositoryParser.V, property.getValue())
.end();
}
public static void main(String argv[]) {
File file = new File("xml1.xml");
XmlReader reader;
XmlWriter writer;
XmlDocument document;
String xmlout;
// Construct a document and parse it
System.out.println("We are going to parse from " + file + ".");
System.out.println("The parser will be set to verbose mode\n");
document = new XmlDocument(file);
reader = new XmlReader();
reader.setVerbose(true);
try {
reader.parse(document);
} catch (Exception e) {
e.printStackTrace();
}
int errors = reader.getErrorCount();
int warnings = reader.getWarningCount();
System.err.println("Completed: " + errors + " errors, " + warnings + " warnings");
if (errors > 0) {
System.err.println("Unrecoverable errors in XML. Stop.");
return;
}
// Now print it
System.out.println("\nHaving parsed the document, we will print it out.");
System.out.println("Here is the DTD:\n");
writer = new XmlWriter();
Writer out = new OutputStreamWriter(System.out);
try {
writer.writeDTD(document, out);
} catch (Exception e) {
e.printStackTrace();
}
System.out.println("\nHere is the XML:\n");
try {
writer.write(document, out);
} catch (Exception e) {
e.printStackTrace();
}
}
private static void toXml(XmlWriter w, Requirement requirement) throws IOException {
w.element(RepositoryParser.REQUIRE)
.attribute(RepositoryParser.NAME, requirement.getName())
.attribute(RepositoryParser.FILTER, requirement.getFilter())
.attribute(RepositoryParser.EXTEND, Boolean.toString(requirement.isExtend()))
.attribute(RepositoryParser.MULTIPLE, Boolean.toString(requirement.isMultiple()))
.attribute(RepositoryParser.OPTIONAL, Boolean.toString(requirement.isOptional()))
.text(requirement.getComment().trim())
.end();
}
private static void toXml(XmlWriter w, Repository repository) throws IOException {
SimpleDateFormat format = new SimpleDateFormat("yyyyMMddhhmmss.SSS");
w.element(RepositoryParser.REPOSITORY)
.attribute(RepositoryParser.NAME, repository.getName())
.attribute(
RepositoryParser.LASTMODIFIED, format.format(new Date(repository.getLastModified())));
if (repository instanceof RepositoryImpl) {
Referral[] referrals = ((RepositoryImpl) repository).getReferrals();
for (int i = 0; referrals != null && i < referrals.length; i++) {
w.element(RepositoryParser.REFERRAL)
.attribute(RepositoryParser.DEPTH, new Integer(referrals[i].getDepth()))
.attribute(RepositoryParser.URL, referrals[i].getUrl())
.end();
}
}
Resource[] resources = repository.getResources();
for (int i = 0; resources != null && i < resources.length; i++) {
toXml(w, resources[i]);
}
w.end();
}
