List of usage examples for org.jdom2 Element Element
public Element(final String name)
From source file:com.athena.chameleon.engine.core.PDFDocGenerator.java
License:Apache License
/** * ?? ? ?// w w w . j a v a 2 s. co m * * @param data * @param upload * @return */ public static List<Element> setExceptionData(PDFMetadataDefinition data, Upload upload) { List<Element> childs = new ArrayList<Element>(); Element section; for (ExceptionInfo comm : data.getExceptionInfoList()) { section = new Element("section"); section.setAttribute("title", comm.getLocation()); if (comm.getComments() != null && comm.getComments().length() > 0) section.addContent(new Element("text").setText(comm.getComments())); section.addContent(new Element("box").setText(comm.getStackTrace())); childs.add(section); } return childs; }
From source file:com.bc.fiduceo.reader.airs.EosCoreMetaParser.java
License:Open Source License
Element parseFromString(String text) {
Element rootElem = new Element("odl");
Element current = rootElem;/*from w w w.j ava 2 s.co m*/
StringTokenizer lineFinder = new StringTokenizer(text, "\n");
while (lineFinder.hasMoreTokens()) {
String line = lineFinder.nextToken();
line = line.trim();
if (line.isEmpty()) {
continue;
}
if (line.startsWith("GROUP")) {
if (line.contains("GROUPTYPE")) {
continue;
}
current = this.startGroup(current, line);
} else if (line.startsWith("OBJECT")) {
current = this.startObject(current, line);
} else if (line.startsWith("END_OBJECT")) {
this.endObject(current, line);
current = current.getParentElement();
} else if (line.startsWith("END_GROUP")) {
this.endGroup(current, line);
current = current.getParentElement();
} else {
this.addField(current, line);
}
}
return rootElem;
}
From source file:com.bc.fiduceo.reader.airs.EosCoreMetaParser.java
License:Open Source License
private Element startGroup(Element parent, String line) { StringTokenizer stoke = new StringTokenizer(line, "="); String toke = stoke.nextToken(); assert toke.equals("GROUP"); String name = stoke.nextToken(); Element group = new Element(name); parent.addContent(group);/*from www. j a va 2s . c o m*/ return group; }
From source file:com.bc.fiduceo.reader.airs.EosCoreMetaParser.java
License:Open Source License
private Element startObject(Element parent, String line) { StringTokenizer stoke = new StringTokenizer(line, "="); String toke = stoke.nextToken(); assert toke.equals("OBJECT"); String name = stoke.nextToken(); Element obj = new Element(name); parent.addContent(obj);// w ww . j av a2 s.c o m return obj; }
From source file:com.bc.fiduceo.reader.airs.EosCoreMetaParser.java
License:Open Source License
private void addField(Element parent, String line) { StringTokenizer stoke = new StringTokenizer(line, "="); String name = stoke.nextToken(); if (stoke.hasMoreTokens()) { Element field = new Element(name); parent.addContent(field);//from w w w.j a v a2 s. co m String value = stoke.nextToken(); if (value.startsWith("(")) { this.parseValueCollection(field, value); return; } value = this.stripQuotes(value); field.addContent(value); } }
From source file:com.bc.fiduceo.reader.airs.EosCoreMetaParser.java
License:Open Source License
private void parseValueCollection(Element field, String value) { if (value.startsWith("(")) { value = value.substring(1);// w w w . j a va2 s . c o m } if (value.endsWith(")")) { value = value.substring(0, value.length() - 1); } StringTokenizer stoke = new StringTokenizer(value, "\","); while (stoke.hasMoreTokens()) { field.addContent((new Element("value")).addContent(this.stripQuotes(stoke.nextToken()))); } }
From source file:com.bio4j.neo4jdb.model.util.GoUtil.java
License:Open Source License
/** * /*www . ja va 2s . co m*/ * @param proteins * @param slimSetXML * @param manager * @param goAnnotationXML * @return GO Slim in xml format */ public static GOSlimXML getGoSlim(ArrayList<ProteinXML> proteins, SlimSetXML slimSetXML, Bio4jManager manager, GoAnnotationXML goAnnotationXML) { GOSlimXML goSlimXML = new GOSlimXML(); if (goAnnotationXML == null) { goAnnotationXML = GoUtil.getGoAnnotation(proteins, manager); } //int goTermsLostNotIncludedInSlimSet = 0; Index<Node> goTermIdIndex = manager.getGoTermIdIndex(); if (goAnnotationXML != null) { List<GoTermXML> goAnnotators = goAnnotationXML.getAnnotatorGoTerms(); //IndexService indexService = manager.getIndexService(); // in this hash map there is one entry for each annotator go term // the hash-set contains every slim-set go term including the annotator HashMap<String, HashSet<String>> goAnnotatorsIncludingSlimSetTermsMap = new HashMap<String, HashSet<String>>(); //Here are the xml elements of the Go terms from the slim set termid --> term xml HashMap<String, GoTermXML> slimSetGos = new HashMap<String, GoTermXML>(); //Here are the number of proteins annotated for each go term of the slim set termid --> number of proteins annotated HashMap<String, Integer> slimSetTermsAnnotationCounts = new HashMap<String, Integer>(); //Now I extract the ids of the SlimSet List<Element> slimElements = slimSetXML.asJDomElement().getChildren(GoTermXML.TAG_NAME); for (Element slimElement : slimElements) { GoTermXML tempGo = new GoTermXML(slimElement); //--completing data of slimset go terms----- GoTermNode tempGoNode = new GoTermNode( manager.getGoTermIdIndex().get(GoTermNode.GO_TERM_ID_INDEX, tempGo.getId()).getSingle()); tempGo.setAspect(tempGoNode.getNamespace()); tempGo.setGoName(tempGoNode.getName()); //------------------------ slimSetGos.put(tempGo.getId(), tempGo); //initializing annotation counts map slimSetTermsAnnotationCounts.put(tempGo.getId(), 0); } //-------------------------------------------- // logger.log(Level.INFO, "slimsetIds:"); // for (String slimId : slimSetIds) { // logger.log(Level.INFO, ("slimId:" + slimId)); // } //Now it is time for goAnnotatorsIncludingSlimSetTermsMap initialization for (GoTermXML goAnnotator : goAnnotators) { goAnnotatorsIncludingSlimSetTermsMap.put(goAnnotator.getId(), new HashSet<String>()); } //------------------------------------------------------ try { IsAGoRel goParentRel = new IsAGoRel(null); //Now I search the way up of every go Annotator and check if in the way I find //any of the terms included in the slim set. //logger.log(Level.INFO, "lalalala"); int callCounter = 0; for (GoTermXML goAnnotator : goAnnotators) { //this array includes the term own id and every ancestor id HashSet<String> ancestorsIds = new HashSet<String>(); GoTermNode goTermNode = new GoTermNode( goTermIdIndex.get(GoTermNode.GO_TERM_ID_INDEX, goAnnotator.getId()).getSingle()); //logger.log(Level.INFO, goTermNode.toString()); fillUpAncestorIds(goTermNode, ancestorsIds, goParentRel, manager.getIsAGoRelIndex(), callCounter); for (String ancestorId : ancestorsIds) { //If the ancestor is included in the slim set, it means that this term //from the slim set includes the goAnnotator if (slimSetGos.keySet().contains(ancestorId)) { HashSet<String> hashSet = goAnnotatorsIncludingSlimSetTermsMap.get(goAnnotator.getId()); hashSet.add(ancestorId); //ancestorId is actually one of the slim-set terms ids. } } callCounter++; } //So now I should have every goAnnotator with its corresponing slimSet terms List<Element> proteinList = goAnnotationXML.getProteinAnnotations() .getChildren(ProteinXML.TAG_NAME); Element proteinsElem = new Element(GOSlimXML.PROTEINS_TAG_NAME); int sampleAnnotatedGeneNumber = 0; for (Element currentElem : proteinList) { boolean annotated = false; //getting the protein ProteinXML currentProteinXML = new ProteinXML(currentElem); //initializing inductors map HashMap<String, String> currentProteinSlimTermInductors = new HashMap<String, String>(); //proteinSlimTermsAndInductorTermsMap.put(currentProteinXML.getId(), currentProteinSlimTermInductors); //System.out.println("currentProteinXML.getId() = " + currentProteinXML.getId()); //--------now we access to its go annotations------------- List<GoTermXML> proteinTerms = new ArrayList<GoTermXML>(); List<GoTermXML> bpTerms = currentProteinXML.getBiologicalProcessGoTerms(); List<GoTermXML> ccTerms = currentProteinXML.getCellularComponentGoTerms(); List<GoTermXML> mfTerms = currentProteinXML.getMolecularFunctionGoTerms(); if (bpTerms != null) { proteinTerms.addAll(bpTerms); } if (ccTerms != null) { proteinTerms.addAll(ccTerms); } if (mfTerms != null) { proteinTerms.addAll(mfTerms); } //------------------------------------------------------ //creating the result xml protein ProteinXML proteinResult = new ProteinXML(); proteinResult.setId(currentProteinXML.getId()); HashSet<String> proteinSlimTems = new HashSet<String>(); for (GoTermXML goTermXML : proteinTerms) { HashSet<String> hashSet = goAnnotatorsIncludingSlimSetTermsMap.get(goTermXML.getId()); System.out.println(""); if (hashSet != null) { if (hashSet.size() > 0) { proteinSlimTems.addAll(hashSet); for (String tempSlimTermId : hashSet) { currentProteinSlimTermInductors.put(tempSlimTermId, goTermXML.getId()); } annotated = true; } else { //-----The go term annotation lost is stored------- goSlimXML.addGoTermLostNotIncludedInSlimSet( new GoTermXML((Element) goTermXML.asJDomElement().clone())); System.out.println("holaaa!" + goTermXML.getId()); } } } //now we get the info from the slimset go terms for (String string : proteinSlimTems) { //logger.log(Level.INFO, ("string: " + string)); GoTermXML tempGoTerm = new GoTermXML( (Element) slimSetGos.get(string).asJDomElement().clone()); //------Adding protein annotation term leading to slim set term ----------- String termInductorId = currentProteinSlimTermInductors.get(tempGoTerm.getId()); //look for inductor info for (GoTermXML goTermXML : proteinTerms) { //System.out.println("goTermXML = " + goTermXML); if (goTermXML.getId().equals(termInductorId)) { tempGoTerm.setProteinAnnotationLeadingToSlimTerm( new GoTermXML((Element) goTermXML.asJDomElement().clone())); break; } } //-------------------------------------------------------------------------- //logger.log(Level.INFO, ("tempGoTerm: " + tempGoTerm)); proteinResult.addGoTerm(tempGoTerm, true); //updating annotation counts slimSetTermsAnnotationCounts.put(string, slimSetTermsAnnotationCounts.get(string) + 1); } proteinsElem.addContent(proteinResult.asJDomElement()); if (annotated) { sampleAnnotatedGeneNumber++; } } //updating slimset annotation counts List<Element> slimSetElems = slimSetXML.asJDomElement().getChildren(GoTermXML.TAG_NAME); for (Element slimSetElem : slimSetElems) { GoTermXML slimSetGo = new GoTermXML(slimSetElem); slimSetGo.setAnnotationsCount(slimSetTermsAnnotationCounts.get(slimSetGo.getId())); } goSlimXML.asJDomElement().addContent(proteinsElem); slimSetXML.detach(); goSlimXML.setSlimSet(slimSetXML); goSlimXML.setSampleGeneNumber(proteinList.size()); goSlimXML.setSampleAnnotatedGeneNumber(sampleAnnotatedGeneNumber); //goSlimXML.set } catch (Exception e) { logger.log(Level.SEVERE, e.getMessage()); StackTraceElement[] trace = e.getStackTrace(); for (StackTraceElement stackTraceElement : trace) { logger.log(Level.SEVERE, stackTraceElement.toString()); } goSlimXML = null; } } else { goSlimXML = null; } return goSlimXML; }
From source file:com.cats.version.VersionCfgParseAndSave.java
License:Apache License
public boolean saveVersionInfo(List<VersionInfo> infos, String fullPath) { try {//from w w w. j a v a 2 s . c o m Document doc = new Document(); Element root = new Element("software-group"); for (VersionInfo info : infos) { Element softEle = new Element("software"); softEle.setAttribute("name", info.getAppName()); Element versionCodeEle = new Element("latest-version-code"); Element versionNameEle = new Element("latest-version"); Element versionPathEle = new Element("latest-version-abspath"); Element startupNameEle = new Element("latest-version-startup"); versionCodeEle.setText(String.valueOf(info.getVersionCode())); versionNameEle.setText(info.getVersion()); versionPathEle.setText(info.getPath()); startupNameEle.setText(info.getStartupName()); softEle.addContent(versionCodeEle); softEle.addContent(versionNameEle); softEle.addContent(versionPathEle); softEle.addContent(startupNameEle); List<VersionInfoDetail> details = info.getDetails(); if (null != details) { Element detailEles = new Element("latest-version-detail"); for (VersionInfoDetail verDetail : details) { Element itemElem = new Element("item"); itemElem.setAttribute("name", verDetail.getTitle()); List<String> detailList = verDetail.getDetail(); for (String detailInfo : detailList) { Element detailEle = new Element("detail"); detailEle.setText(detailInfo); itemElem.addContent(detailEle); } detailEles.addContent(itemElem); } softEle.addContent(detailEles); } List<String> ignoreFiles = info.getIgnoreFiles(); if (ignoreFiles != null) { Element ignoreEles = new Element("ignore-files"); for (String ignoreInfo : ignoreFiles) { Element ignoreItemEle = new Element("item"); ignoreItemEle.setText(ignoreInfo); ignoreEles.addContent(ignoreItemEle); } softEle.addContent(ignoreEles); } root.addContent(softEle); } doc.setRootElement(root); //Save to xml file XMLOutputter xmlOut = null; FileOutputStream fos = null; try { fos = new FileOutputStream(fullPath); xmlOut = new XMLOutputter(Format.getPrettyFormat()); xmlOut.output(doc, fos); } catch (Exception e) { e.printStackTrace(); } finally { if (null != fos) { try { fos.close(); } catch (Exception e) { e.printStackTrace(); } } } } catch (Exception e) { e.printStackTrace(); return false; } return true; }
From source file:com.collir24.policyextractor.Extract.java
License:Apache License
private static Document buildDocument(List<ModulePermissions> modulePermissions) { Element modulePolicy = new Element("modulePolicy"); for (ModulePermissions mps : modulePermissions) { Element module = new Element("module"); module.setAttribute("name", mps.getModuleName()); Set<String> policySet = new HashSet<String>(); for (ModulePermission mp : mps.getPermissions()) { Element permRequired = new Element("permRequired"); permRequired.setAttribute("line", Integer.toString(mp.getLine())); permRequired.setAttribute("className", mp.getClassName()); for (String s : mp.getPolicy()) { Element perm = new Element("perm"); perm.setText(s);//w w w .j a v a 2 s.c o m permRequired.addContent(perm); } module.addContent(permRequired); // TODO: say what caused the permission to be required - see key policySet.addAll(mp.getPolicy()); } CDATA policyData = new CDATA(generatePolicy(policySet)); module.addContent(policyData); modulePolicy.addContent(module); } return new Document(modulePolicy); }
From source file:com.compomics.pladipus.core.control.updates.ProcessingBeanUpdater.java
/** * Adds a new class to the bean definition * @param fullyDefinedClassName the fully defined class name * @throws IllegalArgumentException//from w w w. ja v a 2s .co m * @throws IOException * @throws JDOMException */ public void addNewProcessingStep(String fullyDefinedClassName) throws IllegalArgumentException, IOException, JDOMException { String className = fullyDefinedClassName.substring(fullyDefinedClassName.lastIndexOf(".") + 1); SAXBuilder builder = new SAXBuilder(); Document document = builder.build(beanXMLDefinitionFile); //check if the class is not already in there for (Element aBean : document.getRootElement().getChildren()) { if (aBean.getAttribute("class").getValue().equals(fullyDefinedClassName)) { throw new IllegalArgumentException( "Class is already defined in the bean configuration for " + aBean.getAttributeValue("id")); } else if (aBean.getAttribute("id").getValue().equals(className)) { throw new IllegalArgumentException("Classname is already in use"); } } Element newClassElement = new Element("bean").setAttribute("id", className) .setAttribute("class", fullyDefinedClassName).setAttribute("lazy-init", "true"); document.getRootElement().addContent(newClassElement); XMLOutputter outputter = new XMLOutputter(); try (StringWriter stringWriter = new StringWriter(); FileWriter writer = new FileWriter(beanXMLDefinitionFile);) { outputter.output(document, stringWriter); String output = stringWriter.getBuffer().toString(); //remove empty namespaces output = output.replace(" xmlns=\"\"", ""); writer.append(output); } }