Java OWLObject.equals方法代码示例

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
public void calculateSimilarityAllByAll(String similarityAlgorithmName, Double minScore) throws SimilarityAlgorithmException {
	Set<OWLObject> objs = graph.getAllOWLObjects();
	if (comparisonSuperclass != null) {
		System.out.println("finding descendants of :"+comparisonSuperclass);
		objs = graph.getDescendants(comparisonSuperclass);
		System.out.println("  descendants  :"+objs.size());
	}
	for (OWLObject a : objs) {
		if (excludeObjectFromComparison(a))
			continue;
		for (OWLObject b : graph.getAllOWLObjects()) {
			if (a.equals(b))
				continue;
			if (excludeObjectFromComparison(b))
				continue;
			System.out.println("COMPARE:"+label(a)+" -vs- "+label(b));
			Similarity s = this.getSimilarityAlgorithm(similarityAlgorithmName);
			calculateSimilarity(s,a,b);
			Double sc = s.score;
			if (minScore == null || sc > minScore) {
				System.out.println(a+" "+b+" = "+sc);
				s.print();
			}
		}
	}
}
 

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
public void render(OWLGraphWrapper g) {
	
	if (isWriteHeader) {
		print("IRI");
		sep();
		print("label");
		sep();
		print("definition");
		nl();
	}
	graph = g;
	
	Set<OWLObject> objs = new HashSet<OWLObject>(g.getSourceOntology().getClassesInSignature(Imports.EXCLUDED));
	objs.addAll(g.getSourceOntology().getIndividualsInSignature(Imports.EXCLUDED));

	for (OWLObject obj : objs) {
		if (obj.equals(g.getDataFactory().getOWLNothing()))
			continue;
		if (obj.equals(g.getDataFactory().getOWLThing()))
			continue;
		if (obj instanceof OWLNamedObject)
			render((OWLNamedObject)obj);
	}
	stream.close();
}
 

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
public void render(OWLGraphWrapper g) {
	graph = g;
	
	Set<OWLObject> objs = new HashSet<OWLObject>(g.getSourceOntology().getClassesInSignature(Imports.EXCLUDED));
	objs.addAll(g.getSourceOntology().getIndividualsInSignature(Imports.EXCLUDED));

	for (OWLObject obj : objs) {
		if (obj.equals(g.getDataFactory().getOWLNothing()))
			continue;
		if (obj.equals(g.getDataFactory().getOWLThing()))
			continue;
		if (obj instanceof OWLNamedObject)
			render((OWLNamedObject)obj);
	}
	stream.close();
}
 

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
public boolean isExcludeEdge(OWLGraphEdge edge) {

		if (config.graphEdgeExcludeSet != null ||
				config.graphEdgeIncludeSet != null) {
			for (OWLQuantifiedProperty qp : edge.getQuantifiedPropertyList()) {
				if (isExcluded(qp)) {
					LOG.debug("excluded:"+edge+" based on: "+qp);
					return true;
				}
			}
		}

		OWLObject t = edge.getTarget();
		if (t != null) {
			if (t instanceof OWLNamedObject) {
				OWLNamedObject nt = (OWLNamedObject) t;
				// TODO
				if (nt.getIRI().toString().startsWith("http://www.ifomis.org/bfo"))
					return true;
				if (t instanceof OWLClass && t.equals(getDataFactory().getOWLThing())) {
					return true;
				}

			}
		}
		return false;
	}
 

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
@Test
public void testDescendantsQuery() throws Exception {
	OWLGraphWrapper  g =  getOntologyWrapper();
	OWLClass c = g.getOWLClass("http://example.org#organism");
	OWLObject i = g.getOWLObject("http://example.org#o1");
	boolean ok = false;
	for (OWLObject e : g.queryDescendants(c)) {
		if (RENDER_ONTOLOGY_FLAG) {
			System.out.println("ORG:" + e);
		}
		if (e.equals(i))
			ok = true;
	}
	assertTrue(ok);
}
 

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
@Test
public void testDescendantsQuery() throws Exception {
	OWLGraphWrapper  g =  getOntologyWrapper();
	OWLClass c = g.getOWLClass("http://purl.obolibrary.org/obo/NCBITaxon_10090");
	OWLObject i = g.getOWLObject("http://purl.obolibrary.org/obo/MGI_101761");
	System.out.println("Expecting "+i);
	boolean ok = false;
	for (OWLObject e : g.queryDescendants(c)) {
		System.out.println("ORG:"+e);
		if (e.equals(i))
			ok = true;
	}
	assertTrue(ok);
}
 

import org.semanticweb.owlapi.model.OWLObject; //导入方法依赖的package包/类
/**
 * Given a query object (e.g. organism, disorder, gene), find candidate hit objects based
 * on simple attribute overlap
 * 
 * @param queryObj
 * @return list of objects
 */
public List<OWLObject> search(OWLObject queryObj) {
	List<OWLObject> hits = new ArrayList<OWLObject>(maxHits);
	System.out.println("gettings atts for "+queryObj+" -- "+simEngine.comparisonProperty);
	Set<OWLObject> atts = simEngine.getAttributeClosureFor(queryObj);
	System.out.println("all atts: "+atts.size());
	if (atts.size() == 0)
		return hits;
	
	// only compare using significant atts;
	// we don't do the same test on candidates as these will be removed by the
	// intersection operation. they will have a small effect on the score, as
	// we don't divide by the union, but instead the sum of sizes
	atts = filterNonSignificantAttributes(atts);
	System.out.println("filtered atts: "+atts.size());

	//bloomFilter = new BloomFilter<OWLObject>(0.05, atts.size());
	//bloomFilter.addAll(atts);
			
	SortedMap<Integer,Set<OWLObject>> scoreCandidateMap = new TreeMap<Integer,Set<OWLObject>>();
	
	for (OWLObject candidate : getCandidates()) {
		if (candidate.equals(queryObj))
			continue;
		Set<OWLObject> iAtts = simEngine.getAttributeClosureFor(candidate);
		//Set<OWLObject> iAtts = simEngine.getGraph().getAncestors(candidate);

		if (iAtts.size() == 0)
			continue;
		int cAttsSize = iAtts.size();

		iAtts.retainAll(atts);
		//Collection<OWLObject> iAtts = bloomFilter.intersection(cAtts);
		
		// simJ, one-sided, scaled by 1000
		// negate to ensure largest first
		//Integer score = - (iAtts.size() * 1000 / cAttsSize);
		
		// this biases us towards genes with large numbers of annotations,
		// but it is better at finding the models that share all features
		Integer score = - iAtts.size();
		if (!scoreCandidateMap.containsKey(score)) 
			scoreCandidateMap.put(score, new HashSet<OWLObject>());
		scoreCandidateMap.get(score).add(candidate);
		reporter.report(this,"query_candidate_overlap_total",queryObj,candidate,iAtts.size(),cAttsSize);
	}
	
	int n = 0;
	for (Set<OWLObject> cs : scoreCandidateMap.values()) {
		n += cs.size();
		hits.addAll(cs);
	}
	
	n = 0;
	for (OWLObject hit : hits) {
		n++;
		reporter.report(this,"query_hit_rank_threshold",queryObj,hit,n,maxHits);
	}
	if (hits.size() > maxHits)
		hits = hits.subList(0, maxHits);
	


	return hits;
}