-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #371 from MassBank/release-2.2.2
Release 2.2.2
- Loading branch information
Showing
40 changed files
with
99,802 additions
and
433 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
139 changes: 139 additions & 0 deletions
139
MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| package massbank; | ||
|
|
||
| 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; | ||
|
|
||
| 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; | ||
|
|
||
|
|
||
| /** | ||
| * 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; | ||
|
|
||
| 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()); | ||
| // } | ||
|
|
||
|
|
||
| // 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); | ||
| } | ||
|
|
||
| public static CVUtil get(){ | ||
| CVUtil result = instance; | ||
| if (result == null) { | ||
| synchronized (mutex) { | ||
| result = instance; | ||
| if (result == null) | ||
| instance = result = new CVUtil(); | ||
| } | ||
| } | ||
| return result; | ||
| } | ||
|
|
||
| // public boolean containsTerm(String name) { | ||
| // return ontology.containsTerm(name); | ||
| // } | ||
| // | ||
| // public Term getTerm(String name) { | ||
| // Term term = ontology.getTerm(name); | ||
| // return term; | ||
| // } | ||
|
|
||
| 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()); | ||
| // | ||
|
|
||
| // assertTrue(getAnnotationForTerm(ontology).containsProperty(NAMESPACE)); | ||
| // assertEquals("sequence", getAnnotationForTerm(ontology).getProperty(NAMESPACE)); | ||
| // getAnnotationForTerm(ontology).getProperty(NAMESPACE) | ||
| // //(List<String>) getAnnotationForTerm(ontology).getProperty(ALT_ID); | ||
|
|
||
|
|
||
|
|
||
|
|
||
| return true; | ||
| } | ||
|
|
||
| } |
Oops, something went wrong.