Java Code Examples for org.jdom.Element#setNamespace()

static Algorithm getAlgorithm(AnalysisProperties properties) {
	Algorithm algorithm = null;
	Element para = new Element("analysis");

	String sim = properties.getSim();
	para.setNamespace(Namespace.getNamespace("http://www.async.ece.utah.edu/iBioSim"));
	if (properties.isOde()) {
		if (sim.contains("euler")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_EULER);
		} else if (sim.contains("rk8pd")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND);
		} else if (sim.contains("rkf45") || sim.contains("Runge-Kutta-Fehlberg")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_FEHLBERG);
			para.setAttribute("method", sim);
		} else {
			algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_FEHLBERG);
			para.setAttribute("method", sim);
		}
	} else if (properties.isSsa()) {
		if (sim.equals("gillespie")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_GILLESPIE_DIRECT);
		}

		else if (sim.contains("Mixed")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_DFBA_SOA);
		} else if (sim.contains("Hierarchical")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_GILLESPIE_DIRECT);
		} else if (sim.contains("SSA-CR")) {
			algorithm = new Algorithm(GlobalConstants.KISAO_SSA_CR);
		} else {
			algorithm = new Algorithm(GlobalConstants.KISAO_GILLESPIE_DIRECT);
			para.setAttribute("method", sim);
			if (sim.equals("iSSA")) {
				if (properties.getIncrementalProperties().isMpde()) {
					para.setAttribute("type", "mpde");
				} else if (properties.getIncrementalProperties().isMeanPath()) {
					para.setAttribute("type", "meanPath");
				} else if (properties.getIncrementalProperties().isMedianPath()) {
					para.setAttribute("type", "medianPath");
				}
				if (properties.getIncrementalProperties().isAdaptive()) {
					para.setAttribute("adaptive", "true");
				} else {
					para.setAttribute("adaptive", "false");
				}
				para.setAttribute("numPaths", String.valueOf(properties.getIncrementalProperties().getNumPaths()));
			}
		}
	} else if (properties.isFba()) {
		algorithm = new Algorithm(GlobalConstants.KISAO_FBA);
	} else {
		algorithm = new Algorithm(GlobalConstants.KISAO_GENERIC);
		if (properties.isSbml()) {
			para.setAttribute("method", "Model");
		} else if (properties.isDot()) {
			para.setAttribute("method", "Network");
		} else if (properties.isXhtml()) {
			para.setAttribute("method", "Browser");
		} else {
			para.setAttribute("method", sim);
		}
	}
	if (properties.isExpand()) {
		para.setAttribute("abstraction", "Expand Reactions");
	} else if (properties.isAbs()) {
		para.setAttribute("abstraction", "Reaction-based");
	} else if (properties.isNary()) {
		para.setAttribute("abstraction", "State-based");
	}
	para.setAttribute("rapid1", String.valueOf(properties.getAdvancedProperties().getRap1()));
	para.setAttribute("rapid2", String.valueOf(properties.getAdvancedProperties().getRap2()));
	para.setAttribute("qssa", String.valueOf(properties.getAdvancedProperties().getQss()));
	para.setAttribute("maxConc", String.valueOf(properties.getAdvancedProperties().getCon()));
	para.setAttribute("stoichAmp", String.valueOf(properties.getAdvancedProperties().getStoichAmp()));
	Annotation ann = new Annotation(para);
	algorithm.addAnnotation(ann);

	SimulationProperties simProperties = properties.getSimulationProperties();

	AlgorithmParameter ap = new AlgorithmParameter(GlobalConstants.KISAO_MINIMUM_STEP_SIZE, String.valueOf(simProperties.getMinTimeStep()));
	algorithm.addAlgorithmParameter(ap);
	ap = new AlgorithmParameter(GlobalConstants.KISAO_MAXIMUM_STEP_SIZE, String.valueOf(simProperties.getMaxTimeStep()));
	algorithm.addAlgorithmParameter(ap);
	ap = new AlgorithmParameter(GlobalConstants.KISAO_ABSOLUTE_TOLERANCE, String.valueOf(simProperties.getAbsError()));
	algorithm.addAlgorithmParameter(ap);
	ap = new AlgorithmParameter(GlobalConstants.KISAO_RELATIVE_TOLERANCE, String.valueOf(simProperties.getRelError()));
	algorithm.addAlgorithmParameter(ap);
	ap = new AlgorithmParameter(GlobalConstants.KISAO_SEED, String.valueOf(simProperties.getRndSeed()));
	algorithm.addAlgorithmParameter(ap);
	ap = new AlgorithmParameter(GlobalConstants.KISAO_NUMBER_OF_RUNS, String.valueOf(simProperties.getRun() + (simProperties.getStartIndex() - 1)));
	algorithm.addAlgorithmParameter(ap);
	return algorithm;
}
 

/**
 * Output query results as JDOM XML document containing the standard 
 * SPARQL query results XML format (http://www.w3.org/TR/rdf-sparql-XMLres/).
 * Supports both: Variable binding results and Boolean results.
 * 
 * @return A JDOM XML document.
 */
public Document toXML()
{
	Element sparql = new Element("sparql");
	sparql.setNamespace(Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
	
	// generate head
	Element head = new Element("head");
	if(!bindings.isEmpty()) {
		QueryBinding top = bindings.get(0);
		for(QueryArgument arg : top.getBoundArgs()) {
			if(arg.isVar()) {
				Element var = new Element("variable");
				var.setAttribute("name", arg.getValueAsString());
				head.addContent(var);
			}
		}
	}
	sparql.addContent(head);
	
	if(query.isAsk()) {
		Element booleanElement = new Element("boolean");
		if(ask) {
			booleanElement.setText("true");
		}
		else {
			booleanElement.setText("false");
		}
		sparql.addContent(booleanElement);
	}
	else {
		// otherwise generate results
		Element results = new Element("results");
		for(QueryBinding binding : bindings) {
			Element result = new Element("result");
			for(QueryArgument key : binding.getBoundArgs()) {
				if(key.isVar()) {
					Element b = new Element("binding");
					b.setAttribute("name", key.getValueAsString());
					QueryArgument value = binding.get(key);
					switch(value.getType()) {
					case URI:
						Element uri = new Element("uri");
						uri.setText(value.getValueAsIRI().toString());
						b.addContent(uri);
						break;
					case LITERAL:
						Element literal = new Element("literal");
						literal.setText(value.getValueAsLiteral().getLiteral());
						b.addContent(literal);
						break;
					case BNODE:
						Element bnode = new Element("bnode");
						bnode.setText(value.getValueAsBNode().getID().toString());
						b.addContent(bnode);
						break;
					default:
					}
					result.addContent(b);
				}
			}
			results.addContent(result);
		}
		sparql.addContent(results);
	}
	
	return new Document(sparql);
}
 

public static void propagateNamespace(Element element, Namespace namespace) {
    element.setNamespace(namespace);
    for (Object childElement : element.getChildren()) {
        propagateNamespace((Element) childElement, namespace);
    }
}
 

private void setNamespace(Element element, Namespace namespace) {
	element.setNamespace(namespace);
	for (Iterator iter = element.getChildren().iterator(); iter.hasNext();) {
		setNamespace((Element)iter.next(), namespace);
	}
}