private void translateState(State state, OWLNamedIndividual owlState) {
   this.stateToOWLMap.put(state, owlState);
   this.addClass(owlState, this.factory.getOWLClass(IRI.create(CDAO.STANDARD_STATE)));
   if (StringUtils.isNotBlank(state.getLabel())) {
     final OWLLiteral label = this.factory.getOWLLiteral(state.getLabel());
     this.addAnnotation(OWLRDFVocabulary.RDFS_LABEL.getIRI(), owlState.getIRI(), label);
   }
   if (StringUtils.isNotBlank(state.getComment())) {
     final OWLLiteral comment = factory.getOWLLiteral(state.getComment());
     this.addAnnotation(OWLRDFVocabulary.RDFS_COMMENT.getIRI(), owlState.getIRI(), comment);
   }
   int phenotypeIndex = 0;
   final OWLObjectProperty denotes = this.factory.getOWLObjectProperty(IRI.create(IAO.DENOTES));
   for (Phenotype phenotype : state.getPhenotypes()) {
     phenotypeIndex++;
     final IRI phenotypeIRI =
         IRI.create(owlState.getIRI().toURI().toString() + "/phenotype/" + phenotypeIndex);
     final OWLClass owlPhenotype = this.factory.getOWLClass(phenotypeIRI);
     final OWLObjectAllValuesFrom denotesOnlyPhenotype =
         this.factory.getOWLObjectAllValuesFrom(denotes, owlPhenotype);
     this.ontologyManager.addAxiom(
         ontology, this.factory.getOWLClassAssertionAxiom(denotesOnlyPhenotype, owlState));
     this.translatePhenotype(phenotype, owlPhenotype);
   }
 }
Ejemplo n.º 2
0
 private void deleteSelectedPhenotype() {
   final State state = this.getSelectedState();
   if (state != null) {
     final Phenotype phenotype = this.getSelectedPhenotype();
     if (phenotype != null) {
       state.removePhenotype(phenotype);
     }
   }
 }
Ejemplo n.º 3
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 private void addPhenotype() {
   final State state = this.getSelectedState();
   if (state != null) {
     final Phenotype phenotype = state.newPhenotype();
     phenotype.setEntity(this.getAutofillEntity());
     final OBOClass possibleQuality = this.getAutofillQuality();
     if ((possibleQuality != null) && (possibleQuality.getID().equals(COUNT))) {
       phenotype.setQuality(this.getAutofillQuality());
     }
   }
 }
 private void translateMatrixCell(
     Taxon taxon, Character character, State state, OWLNamedIndividual matrixCell) {
   this.addClass(matrixCell, this.factory.getOWLClass(IRI.create(CDAO.MATRIX_CELL)));
   this.addPropertyAssertion(
       IRI.create(CDAO.BELONGS_TO_CHARACTER), matrixCell, this.characterToOWLMap.get(character));
   this.addPropertyAssertion(
       IRI.create(CDAO.BELONGS_TO_TU), matrixCell, this.taxonOTUToOWLMap.get(taxon));
   this.addPropertyAssertion(
       IRI.create(CDAO.HAS_STATE), matrixCell, this.stateToOWLMap.get(state));
   if (taxon.getValidName() != null) {
     final IRI taxonIRI = this.convertOBOIRI(taxon.getValidName().getID());
     final OWLClass taxonClass = this.factory.getOWLClass(taxonIRI);
     for (Phenotype phenotype : state.getPhenotypes()) {
       final OWLClass eq = this.phenotypeToOWLMap.get(phenotype);
       final OWLObjectProperty exhibits =
           this.factory.getOWLObjectProperty(IRI.create(PHENOSCAPE.EXHIBITS));
       final OWLClassExpression exhibitsSomeEQ =
           this.factory.getOWLObjectSomeValuesFrom(exhibits, eq);
       final OWLAnnotationProperty positedBy =
           this.factory.getOWLAnnotationProperty(IRI.create(PHENOSCAPE.POSITED_BY));
       final OWLAnnotation positedByAnnotation =
           this.factory.getOWLAnnotation(positedBy, matrixCell.getIRI());
       final Set<OWLAnnotation> annotations = Collections.singleton(positedByAnnotation);
       final OWLSubClassOfAxiom annotatedSubClassOfAxiom =
           this.factory.getOWLSubClassOfAxiom(taxonClass, exhibitsSomeEQ, annotations);
       this.ontologyManager.addAxiom(this.ontology, annotatedSubClassOfAxiom);
     }
   }
 }
Ejemplo n.º 5
0
 private OBOClass getAutofillQuality() {
   // check current state
   for (State state : this.getController().getCurrentStatesSelectionModel().getSelected()) {
     for (Phenotype phenotype : state.getPhenotypes()) {
       if (phenotype.getQuality() != null) {
         return phenotype.getQuality();
       }
     }
   }
   // then check all states
   for (State state : this.getController().getStatesForCurrentCharacterSelection()) {
     for (Phenotype phenotype : state.getPhenotypes()) {
       if (phenotype.getQuality() != null) {
         return phenotype.getQuality();
       }
     }
   }
   return null;
 }