/** * Tr. * * @return the oBO doc */ protected OBODoc tr() { setObodoc(new OBODoc()); preProcess(); tr(getOWLOntology()); // declarations need to be sorted - otherwise there is a risk of id being processed before // altId, which causes spurious clauses. accept(getOWLOntology().axioms(AxiomType.DECLARATION).sorted()); AxiomType.skipDeclarations().forEach(t -> accept(getOWLOntology().axioms(t))); if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) { String axiomString = OwlStringTools.translate(untranslatableAxioms, manager); if (!axiomString.isEmpty()) { Frame headerFrame = getObodoc().getHeaderFrame(); if (headerFrame == null) { headerFrame = new Frame(FrameType.HEADER); getObodoc().setHeaderFrame(headerFrame); } headerFrame.addClause(new Clause(OboFormatTag.TAG_OWL_AXIOMS, axiomString)); } } return getObodoc(); }
/** * Tr. * * @return the oBO doc */ protected OBODoc tr() { setObodoc(new OBODoc()); preProcess(); tr(getOWLOntology()); // declarations need to be sorted - otherwise there is a risk of id being processed before // altId, which causes spurious clauses. accept(getOWLOntology().axioms(AxiomType.DECLARATION).sorted()); AxiomType.skipDeclarations().forEach(t -> accept(getOWLOntology().axioms(t))); if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) { String axiomString = OwlStringTools.translate(untranslatableAxioms, manager); if (!axiomString.isEmpty()) { Frame headerFrame = getObodoc().getHeaderFrame(); if (headerFrame == null) { headerFrame = new Frame(FrameType.HEADER); getObodoc().setHeaderFrame(headerFrame); } headerFrame.addClause(new Clause(OboFormatTag.TAG_OWL_AXIOMS, axiomString)); } } return getObodoc(); }
/** * Tr. * * @return the oBO doc */ protected OBODoc tr() { setObodoc(new OBODoc()); preProcess(); tr(getOWLOntology()); // declarations need to be sorted - otherwise there is a risk of id being processed before // altId, which causes spurious clauses. accept(getOWLOntology().axioms(AxiomType.DECLARATION).sorted()); AxiomType.skipDeclarations().forEach(t -> accept(getOWLOntology().axioms(t))); if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) { String axiomString = OwlStringTools.translate(untranslatableAxioms, manager); if (!axiomString.isEmpty()) { Frame headerFrame = getObodoc().getHeaderFrame(); if (headerFrame == null) { headerFrame = new Frame(FrameType.HEADER); getObodoc().setHeaderFrame(headerFrame); } headerFrame.addClause(new Clause(OboFormatTag.TAG_OWL_AXIOMS, axiomString)); } } return getObodoc(); }
/** * Tr. * * @return the oBO doc */ protected OBODoc tr() { setObodoc(new OBODoc()); preProcess(); tr(getOWLOntology()); // declarations need to be sorted - otherwise there is a risk of id being processed before // altId, which causes spurious clauses. accept(getOWLOntology().axioms(AxiomType.DECLARATION).sorted()); AxiomType.skipDeclarations().forEach(t -> accept(getOWLOntology().axioms(t))); if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) { String axiomString = OwlStringTools.translate(untranslatableAxioms, manager); if (!axiomString.isEmpty()) { Frame headerFrame = getObodoc().getHeaderFrame(); if (headerFrame == null) { headerFrame = new Frame(FrameType.HEADER); getObodoc().setHeaderFrame(headerFrame); } headerFrame.addClause(new Clause(OboFormatTag.TAG_OWL_AXIOMS, axiomString)); } } return getObodoc(); }
.forEach(s -> getOwlOntology().add(OwlStringTools.translate( s, manager))); } else {
.forEach(s -> getOwlOntology().add(OwlStringTools.translate( s, manager))); } else {
.forEach(s -> getOwlOntology().add(OwlStringTools.translate( s, manager))); } else {
.forEach(s -> getOwlOntology().add(OwlStringTools.translate( s, manager))); } else {
try { for (String axiomString : axiomStrings) { Set<OWLAxiom> axioms = OwlStringTools.translate(axiomString, manager); if (axioms != null) {
String axiomString = OwlStringTools.translate(untranslatableAxioms, manager); if (axiomString != null) {