Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Clause.addValue()

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                    clause.addValue("xsd:string");
                } else {
                    clause.addValue(dataTypeIri.toString());
                }
            } else if (annVal instanceof IRI) {
                clause.addValue(getIdentifier((IRI) annVal));
            }
            frame.addClause(clause);
        }
        return true;
    }
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                }
                if (cls2 != null) {
                    Clause c = new Clause(
                            OboFormatTag.TAG_INTERSECTION_OF.getTag());
                    if (r != null) {
                        c.addValue(r);
                    }
                    c.addValue(cls2);
                    equivalenceAxiomClauses.add(c);
                    if (exact != null) {
                        String string = exact.toString();
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                    Clause c = new Clause(
                            OboFormatTag.TAG_INTERSECTION_OF.getTag());
                    if (r != null) {
                        c.addValue(r);
                    }
                    c.addValue(cls2);
                    equivalenceAxiomClauses.add(c);
                    if (exact != null) {
                        String string = exact.toString();
                        assert string != null;
                        c.addQualifierValue(new QualifierValue("cardinality",
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            // here we would have a convention that an unprefixed
            // subsetdef/synonymtypedef
            // gets placed in a temp ID space, and only this id space is
            // stripped
            indvId = indvId.replaceFirst(".*:", "");
            c.addValue(indvId);
            c.addValue(indvId);
            String nameValue = "";
            String scopeValue = null;
            for (OWLAnnotation ann : annotations(getOWLOntology()
                    .getAnnotationAssertionAxioms(indv.getIRI()))) {
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            // subsetdef/synonymtypedef
            // gets placed in a temp ID space, and only this id space is
            // stripped
            indvId = indvId.replaceFirst(".*:", "");
            c.addValue(indvId);
            c.addValue(indvId);
            String nameValue = "";
            String scopeValue = null;
            for (OWLAnnotation ann : annotations(getOWLOntology()
                    .getAnnotationAssertionAxioms(indv.getIRI()))) {
                String propId = ann.getProperty().getIRI().toString();
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                    nameValue = '"' + value + '"';
                } else {
                    scopeValue = value;
                }
            }
            c.addValue(nameValue);
            if (scopeValue != null) {
                c.addValue(scopeValue);
            }
            f.addClause(c);
        } else if (IRI_CLASS_SUBSETDEF.equals(clsIRI)) {
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                    scopeValue = value;
                }
            }
            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());
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            // here we would have a convention that an unprefixed
            // subsetdef/synonymtypedef
            // gets placed in a temp ID space, and only this id space is
            // stripped
            indvId = indvId.replaceFirst(".*:", "");
            c.addValue(indvId);
            String nameValue = "";
            for (OWLAnnotation ann : annotations(getOWLOntology()
                    .getAnnotationAssertionAxioms(indv.getIRI()))) {
                String propId = ann.getProperty().getIRI().toString();
                String value = ((OWLLiteral) ann.getValue()).getLiteral();
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                if (OWLRDFVocabulary.RDFS_LABEL.getIRI().toString()
                        .equals(propId)) {
                    nameValue = '"' + value + '"';
                }
            }
            c.addValue(nameValue);
            f.addClause(c);
        } else {
            // TODO: individual
        }
    }
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        f.addClause(cl);
        String id = getParseUntil(" !{");
        if (id.isEmpty()) {
            error("Could not find an valid id, id is empty.");
        }
        cl.addValue(id);
        f.setId(id);
        parseEOL(cl);
    }

    // ----------------------------------------
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