Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Frame.addClause()

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            f.addClause(c);
        }
        String id = getOntologyId(ontology);
        Clause c = new Clause(OboFormatTag.TAG_ONTOLOGY.getTag());
        c.setValue(id);
        f.addClause(c);
        String vid = getDataVersion(ontology);
        if (vid != null) {
            Clause c2 = new Clause(OboFormatTag.TAG_DATA_VERSION.getTag());
            c2.setValue(vid);
            f.addClause(c2);
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        f.addClause(c);
        String vid = getDataVersion(ontology);
        if (vid != null) {
            Clause c2 = new Clause(OboFormatTag.TAG_DATA_VERSION.getTag());
            c2.setValue(vid);
            f.addClause(c2);
        }
        for (OWLAnnotation ann : ontology.getAnnotations()) {
            OWLAnnotationProperty property = ann.getProperty();
            String tagString = owlObjectToTag(property);
            if (OboFormatTag.TAG_COMMENT.getTag().equals(tagString)) {
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        List<Clause> equivalenceAxiomClauses = new ArrayList<>();
        String cls2 = getIdentifier(ce2);
        if (cls2 != null) {
            Clause c = new Clause(OboFormatTag.TAG_EQUIVALENT_TO.getTag());
            c.setValue(cls2);
            f.addClause(c);
            addQualifiers(c, ax.getAnnotations());
        } else if (ce2 instanceof OWLObjectUnionOf) {
            List<OWLClassExpression> list2 = ((OWLObjectUnionOf) ce2)
                    .getOperandsAsList();
            for (OWLClassExpression oce : list2) {
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            error(ax, false);
        }
        // Only add clauses if the *entire* equivalence axiom can be translated
        if (!isUntranslateable) {
            for (Clause c : equivalenceAxiomClauses) {
                f.addClause(c);
            }
        }
    }

    /**
 
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        }
        OWLClass cls1 = ce1.asOWLClass();
        Frame f = getTermFrame(cls1);
        Clause c = new Clause(OboFormatTag.TAG_DISJOINT_FROM.getTag());
        c.setValue(cls2);
        f.addClause(c);
        addQualifiers(c, ax.getAnnotations());
    }

    /**
     * Tr.
 
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        String id = getIdentifier(entity.getIRI());
        Frame f = getObodoc().getTermFrame(id);
        if (f == null) {
            f = new Frame(FrameType.TERM);
            f.setId(id);
            f.addClause(new Clause(OboFormatTag.TAG_ID, id));
            add(f);
        }
        return f;
    }
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        String id = getIdentifier(entity);
        Frame f = getObodoc().getTypedefFrame(id);
        if (f == null) {
            f = new Frame(FrameType.TYPEDEF);
            f.setId(id);
            f.addClause(new Clause(OboFormatTag.TAG_ID, id));
            add(f);
        }
        return f;
    }
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            }
            c.addValue(nameValue);
            if (scopeValue != null) {
                c.addValue(scopeValue);
            }
            f.addClause(c);
        } else if (IRI_CLASS_SUBSETDEF.equals(clsIRI)) {
            Frame f = getObodoc().getHeaderFrame();
            Clause c = new Clause(OboFormatTag.TAG_SUBSETDEF.getTag());
            OWLNamedIndividual indv = (OWLNamedIndividual) ax.getIndividual();
            String indvId = getIdentifier(indv);
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                        .equals(propId)) {
                    nameValue = '"' + value + '"';
                }
            }
            c.addValue(nameValue);
            f.addClause(c);
        } else {
            // TODO: individual
        }
    }
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            Frame f = getTermFrame((OWLClass) sub);
            if (sup instanceof OWLClass) {
                Clause c = new Clause(OboFormatTag.TAG_IS_A.getTag());
                c.setValue(getIdentifier(sup));
                c.setQualifierValues(qvs);
                f.addClause(c);
                addQualifiers(c, ax.getAnnotations());
            } else if (sup instanceof OWLObjectCardinalityRestriction) {
                // OWLObjectExactCardinality
                // OWLObjectMinCardinality
                // OWLObjectMaxCardinality
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