Package org.obolibrary.oboformat.model

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

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        @Override
        public void expand(Frame sf, String id, String xRef) {
            Clause gc = new Clause(OboFormatTag.TAG_INTERSECTION_OF, id);
            Clause dc = new Clause(OboFormatTag.TAG_INTERSECTION_OF);
            dc.setValue(rel);
            dc.addValue(tgt);
            getTargetFrame(xRef).addClause(gc);
            getTargetFrame(xRef).addClause(dc);
        }
    }
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        }

        @Override
        public void expand(Frame sf, String id, String xRef) {
            Clause c = new Clause(OboFormatTag.TAG_RELATIONSHIP, rel);
            c.addValue(xRef);
            getTargetFrame(id).addClause(c);
        }
    }
}
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        @Override
        public void expand(Frame sf, String id, String xRef) {
            Clause gc = new Clause(OboFormatTag.TAG_INTERSECTION_OF, xRef);
            Clause dc = new Clause(OboFormatTag.TAG_INTERSECTION_OF);
            dc.setValue(rel);
            dc.addValue(tgt);
            getTargetFrame(id).addClause(gc);
            getTargetFrame(id).addClause(dc);
        }
    }
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        if (prop == null || value == null) {
            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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                    unprocessedAnnotations.remove(ann);
                    break;
                }
            }
            clause = new Clause(tag);
            clause.addValue(rel1);
            clause.addValue(rel2);
        }
        f.addClause(clause);
        addQualifiers(clause, unprocessedAnnotations);
    }
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                    break;
                }
            }
            clause = new Clause(tag);
            clause.addValue(rel1);
            clause.addValue(rel2);
        }
        f.addClause(clause);
        addQualifiers(clause, unprocessedAnnotations);
    }
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                    scope = owlObjectToTag(axiom.getValue());
                }
            }
            Frame hf = getObodoc().getHeaderFrame();
            Clause clause = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF);
            clause.addValue(getIdentifier(sub));
            clause.addValue(name);
            if (scope != null) {
                clause.addValue(scope);
            }
            addQualifiers(clause, ax.getAnnotations());
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                }
            }
            Frame hf = getObodoc().getHeaderFrame();
            Clause clause = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF);
            clause.addValue(getIdentifier(sub));
            clause.addValue(name);
            if (scope != null) {
                clause.addValue(scope);
            }
            addQualifiers(clause, ax.getAnnotations());
            if (!hf.getClauses().contains(clause)) {
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            Frame hf = getObodoc().getHeaderFrame();
            Clause clause = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF);
            clause.addValue(getIdentifier(sub));
            clause.addValue(name);
            if (scope != null) {
                clause.addValue(scope);
            }
            addQualifiers(clause, ax.getAnnotations());
            if (!hf.getClauses().contains(clause)) {
                hf.addClause(clause);
            } else {
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                    break;
                }
            }
            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);
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