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);
}
}
private void deleteSelectedPhenotype() {
final State state = this.getSelectedState();
if (state != null) {
final Phenotype phenotype = this.getSelectedPhenotype();
if (phenotype != null) {
state.removePhenotype(phenotype);
}
}
}
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);
}
}
}
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;
}