protected void add(@Nullable Frame f) { if (f != null) { try { getObodoc().addFrame(f); } catch (Exception ex) { LOG.error(ex.getMessage(), ex); } } }
protected void add(@Nullable Frame f) { if (f != null) { try { getObodoc().addFrame(f); } catch (Exception ex) { LOG.error(ex.getMessage(), ex); } } }
protected void add(@Nullable Frame f) { if (f != null) { try { getObodoc().addFrame(f); } catch (Exception ex) { LOG.error(ex.getMessage(), ex); } } }
protected void add(@Nullable Frame f) { if (f != null) { try { getObodoc().addFrame(f); } catch (Exception ex) { LOG.error(ex.getMessage(), ex); } } }
private Frame getTermFrame(String id) { 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; }
private Frame getTypedefFrame(String id) { 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; }
/** * 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(); }
private Frame getTermFrame(String id) { 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; }
/** * 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(); }
private Frame getTermFrame(String id) { 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; }
private Frame getTypedefFrame(String id) { 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; }
private Frame getTermFrame(String id) { 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; }
/** * 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(); }
private Frame getTypedefFrame(String id) { 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; }
private Frame getTypedefFrame(String id) { 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; }
getObodoc().setHeaderFrame(f); ontology.directImportsDocuments() .forEach(iri -> f.addClause(new Clause(OboFormatTag.TAG_IMPORT.getTag())
getObodoc().setHeaderFrame(f); ontology.directImportsDocuments() .forEach(iri -> f.addClause(new Clause(OboFormatTag.TAG_IMPORT.getTag())
getObodoc().setHeaderFrame(f); ontology.directImportsDocuments() .forEach(iri -> f.addClause(new Clause(OboFormatTag.TAG_IMPORT.getTag())
getObodoc().setHeaderFrame(f); ontology.directImportsDocuments() .forEach(iri -> f.addClause(new Clause(OboFormatTag.TAG_IMPORT.getTag())