Package org.obolibrary.oboformat.model

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

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                    Frame headerFrame = getObodoc().getHeaderFrame();
                    if (headerFrame == null) {
                        headerFrame = new Frame(FrameType.HEADER);
                        getObodoc().setHeaderFrame(headerFrame);
                    }
                    headerFrame.addClause(new Clause(
                            OboFormatTag.TAG_OWL_AXIOMS, axiomString));
                }
            } catch (OwlStringException e) {
                throw new OWLRuntimeException(e);
            }
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            clause = f.getClause(tag);
            if (tag != null) {
                clause.setValue(value);
            } else {
                clause = new Clause(tag, value);
                f.addClause(clause);
            }
        } else {
            clause = new Clause(tag, value);
            f.addClause(clause);
        }
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                clause = new Clause(tag, value);
                f.addClause(clause);
            }
        } else {
            clause = new Clause(tag, value);
            f.addClause(clause);
        }
        addQualifiers(clause, annotations);
        return true;
    }
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            return false;
        }
        Frame f = getTypedefFrame(prop);
        Clause clause = new Clause(tag);
        clause.addValue(value);
        f.addClause(clause);
        addQualifiers(clause, annotations);
        return true;
    }

    /**
 
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            }
            clause = new Clause(tag);
            clause.addValue(rel1);
            clause.addValue(rel2);
        }
        f.addClause(clause);
        addQualifiers(clause, unprocessedAnnotations);
    }

    /**
     * Tr.
 
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            if (supId.startsWith("owl:")) {
                return;
            }
            Frame f = getTypedefFrame((OWLObjectProperty) sub);
            Clause clause = new Clause(OboFormatTag.TAG_IS_A, supId);
            f.addClause(clause);
            addQualifiers(clause, ax.getAnnotations());
        } else {
            error(ax, true);
        }
    }
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            if (scope != null) {
                clause.addValue(scope);
            }
            addQualifiers(clause, ax.getAnnotations());
            if (!hf.getClauses().contains(clause)) {
                hf.addClause(clause);
            } else {
                LOG.error("duplicate clause: {} in header", clause);
            }
            return;
        } else if (OboFormatTag.TAG_SUBSETDEF.getTag().equals(tagObject)) {
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            Frame hf = getObodoc().getHeaderFrame();
            Clause clause = new Clause(OboFormatTag.TAG_SUBSETDEF);
            clause.addValue(getIdentifier(sub));
            clause.addValue(comment);
            if (!hf.getClauses().contains(clause)) {
                hf.addClause(clause);
            } else {
                LOG.error("duplicate clause: {} in header", clause);
            }
            addQualifiers(clause, ax.getAnnotations());
            return;
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            if (supId.startsWith("owl:")) {
                return;
            }
            Frame f = getTypedefFrame(sub);
            Clause clause = new Clause(OboFormatTag.TAG_IS_A, supId);
            f.addClause(clause);
            addQualifiers(clause, ax.getAnnotations());
        } else {
            error(ax, true);
        }
    }
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        getObodoc().setHeaderFrame(f);
        for (IRI iri : ontology.getDirectImportsDocuments()) {
            Clause c = new Clause(OboFormatTag.TAG_IMPORT.getTag());
            // c.setValue(getOntologyId(iri));
            c.setValue(iri.toString());
            f.addClause(c);
        }
        String id = getOntologyId(ontology);
        Clause c = new Clause(OboFormatTag.TAG_ONTOLOGY.getTag());
        c.setValue(id);
        f.addClause(c);
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