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Merge pull request #371 from MassBank/release-2.2.2
Release 2.2.2
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MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java
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| package massbank; | ||
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| import java.io.BufferedReader; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.io.InputStreamReader; | ||
| import java.net.URISyntaxException; | ||
| import java.net.URL; | ||
| import java.text.ParseException; | ||
| import java.util.ArrayList; | ||
| import java.util.Set; | ||
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| import org.semanticweb.owlapi.apibinding.OWLManager; | ||
| import org.semanticweb.owlapi.model.IRI; | ||
| import org.semanticweb.owlapi.model.OWLAxiom; | ||
| import org.semanticweb.owlapi.model.OWLDataFactory; | ||
| import org.semanticweb.owlapi.model.OWLOntology; | ||
| import org.semanticweb.owlapi.model.OWLOntologyCreationException; | ||
| import org.semanticweb.owlapi.model.OWLOntologyManager; | ||
| import org.semanticweb.owlapi.reasoner.BufferingMode; | ||
| import org.semanticweb.owlapi.reasoner.InferenceType; | ||
| import org.semanticweb.owlapi.reasoner.OWLReasoner; | ||
| import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; | ||
| import org.semanticweb.owlapi.reasoner.SimpleConfiguration; | ||
| import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner; | ||
| import org.semanticweb.owlapi.reasoner.NodeSet; | ||
| import org.semanticweb.owlapi.model.OWLClass; | ||
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| /** | ||
| * Controled vocabulary handler. | ||
| * | ||
| * @author rmeier | ||
| * @version 07-10-2022 | ||
| */ | ||
| public final class CVUtil { | ||
| private static CVUtil instance; | ||
| private static Object mutex = new Object(); | ||
| //Ontology ontology; | ||
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| private CVUtil(){ | ||
| // try (BufferedReader reader = new BufferedReader(new InputStreamReader(getClass().getClassLoader().getResourceAsStream("cv/psi-ms.obo")))) { | ||
| // OboParser parser = new OboParser(); | ||
| // try { | ||
| // ontology = parser.parseOBO(reader, "Mass spectrometry ontology", "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry."); | ||
| // } catch (ParseException ex) { | ||
| // System.err.println("Parsing exception: " + ex.getLocalizedMessage()); | ||
| // } | ||
| // } catch (IOException e) { | ||
| // e.printStackTrace(); | ||
| // } | ||
| // OWLOntologyManager man = OWLManager.createOWLOntologyManager(); | ||
| // OWLOntology o=null; | ||
| // try { | ||
| // o = man.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl")); | ||
| // o = man.loadOntologyFromOntologyDocument(getClass().getClassLoader().getResourceAsStream("cv/psi-ms.owl")); | ||
| // } catch (OWLOntologyCreationException e) { | ||
| // // TODO Auto-generated catch block | ||
| // e.printStackTrace(); | ||
| // } | ||
| // for(OWLAxiom ax:o.getLogicalAxioms()) { | ||
| // System.out.println(ax); | ||
| // } | ||
| // System.out.println("Axioms: "+o.getAxiomCount()+", Format:"+man.getOntologyFormat(o)); | ||
| // ArrayList t = new ArrayList<OWLAxiom>(); | ||
| // for(OWLClass ax:o.getClassesInSignature()) { | ||
| // t.add(ax); | ||
| // System.out.println(ax.getIRI()); | ||
| // } | ||
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| // o.signature().filter((e->(!e.isBuiltIn()&&e.getIRI().getFragment().startsWith("M")))); | ||
| //o.signature().filter((e->(!e.isBuiltIn()&&e.getIRI().getFragment().startsWith("M")))).forEach(System.out::println); | ||
| // System.out.println(o); | ||
| //OWLReasonerFactory rf = new ReasonerFactory(); | ||
| //OWLReasoner r = rf.createReasoner(o); | ||
| // | ||
| // OWLDataFactory df = man.getOWLDataFactory(); | ||
| // OWLReasoner r = new StructuralReasoner(o, new SimpleConfiguration(),BufferingMode.BUFFERING); | ||
| // System.out.println(df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MS_1000044")).getEntityType()); | ||
| // System.out.println(df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MS_1000044")).getIRI()); | ||
| // //NodeSet<OWLClass> result = r.getSuperClasses(df.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/pizza/pizza.owl#Hot")), false); | ||
| // NodeSet<OWLClass> result = r.getSuperClasses(df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MS_1000044")), true); | ||
| // System.out.println(result); | ||
| // ((StructuralReasoner) r).dumpClassHierarchy(false); | ||
| // r.precomputeInferences(InferenceType.CLASS_HIERARCHY); | ||
| // r.getSubClasses(df.getOWLClass("http://purl.obolibrary.org/obo/MS:1000044"), false).forEach(System.out::println); | ||
| } | ||
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| public static CVUtil get(){ | ||
| CVUtil result = instance; | ||
| if (result == null) { | ||
| synchronized (mutex) { | ||
| result = instance; | ||
| if (result == null) | ||
| instance = result = new CVUtil(); | ||
| } | ||
| } | ||
| return result; | ||
| } | ||
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| // public boolean containsTerm(String name) { | ||
| // return ontology.containsTerm(name); | ||
| // } | ||
| // | ||
| // public Term getTerm(String name) { | ||
| // Term term = ontology.getTerm(name); | ||
| // return term; | ||
| // } | ||
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| public boolean termIsA(String name, String isA) { | ||
| // Term term = ontology.getTerm(name); | ||
| // Set<Term> keys = ontology.getTerms(); | ||
| // System.out.println(keys.toString()); | ||
| // System.out.println(term.getName()); | ||
| // System.out.println(term.getDescription()); | ||
| // System.out.println(term.getAnnotation()); | ||
| // System.out.println(term.getSynonyms().toString()); | ||
| // System.out.println(term.getOntology()); | ||
| // System.out.println(term.getOntology()); | ||
| // | ||
| // System.out.println(ontology.getTriples(ontology.getTerm("MS:1003294"), ontology.getTerm("MS:1000250") , ontology.getTerm(IS_A))); | ||
| // System.out.println(ontology.getTriples(ontology.getTerm("MS:1000250"), ontology.getTerm("MS:1003294") , ontology.getTerm(IS_A))); | ||
| // System.out.println(ontology.getTriples(ontology.getTerm("MS:1003294"), ontology.getTerm("MS:1000044") , ontology.getTerm(IS_A))); | ||
| // System.out.println(ontology.getTerm("MS:1003294").getAnnotation()); | ||
| // | ||
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| // assertTrue(getAnnotationForTerm(ontology).containsProperty(NAMESPACE)); | ||
| // assertEquals("sequence", getAnnotationForTerm(ontology).getProperty(NAMESPACE)); | ||
| // getAnnotationForTerm(ontology).getProperty(NAMESPACE) | ||
| // //(List<String>) getAnnotationForTerm(ontology).getProperty(ALT_ID); | ||
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| return true; | ||
| } | ||
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| } |
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