Package org.obolibrary.oboformat.model

Examples of org.obolibrary.oboformat.model.Xref

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                synType = OboFormatTag.TAG_RELATED.getTag();
            }
            ax = fac.getOWLAnnotationAssertionAxiom(trSynonymType(synType),
                    sub, trLiteral(clause.getValue()), annotations);
        } else if (tagConstant == OboFormatTag.TAG_XREF) {
            Xref xref = (Xref) clause.getValue();
            String xrefAnnotation = xref.getAnnotation();
            if (xrefAnnotation != null) {
                OWLAnnotation owlAnnotation = fac.getOWLAnnotation(
                        fac.getRDFSLabel(), fac.getOWLLiteral(xrefAnnotation));
                annotations.add(owlAnnotation);
            }
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                        if (v instanceof IRI) {
                            xrefValue = v.toString();
                        } else {
                            xrefValue = ((OWLLiteral) v).getLiteral();
                        }
                        Xref xref = new Xref(xrefValue);
                        clause.addXref(xref);
                        unprocessedQualifiers.remove(aan);
                    }
                }
            } else if (tag == OboFormatTag.TAG_XREF) {
                Xref xref = new Xref(value);
                for (OWLAnnotation annotation : qualifiers) {
                    if (fac.getRDFSLabel().equals(annotation.getProperty())) {
                        OWLAnnotationValue owlAnnotationValue = annotation
                                .getValue();
                        if (owlAnnotationValue instanceof OWLLiteral) {
                            unprocessedQualifiers.remove(annotation);
                            String xrefAnnotation = ((OWLLiteral) owlAnnotationValue)
                                    .getLiteral();
                            xrefAnnotation = xrefAnnotation.trim();
                            if (!xrefAnnotation.isEmpty()) {
                                xref.setAnnotation(xrefAnnotation);
                            }
                        }
                    }
                }
                clause.setValue(xref);
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                if (v instanceof IRI) {
                    xrefValue = v.toString();
                } else {
                    xrefValue = ((OWLLiteral) v).getLiteral();
                }
                Xref xref = new Xref(xrefValue);
                clause.addXref(xref);
                unprocessedQualifiers.remove(aan);
            } else if (OboFormatTag.TAG_HAS_SYNONYM_TYPE.getTag()
                    .equals(propId)) {
                type = getIdentifier(aan.getValue());
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    public void expandXrefs() {
        for (Frame f : sourceOBODoc.getTermFrames()) {
            String id = f.getTagValue(OboFormatTag.TAG_ID, String.class);
            Collection<Clause> clauses = f.getClauses(OboFormatTag.TAG_XREF);
            for (Clause c : clauses) {
                Xref x = c.getValue(Xref.class);
                if (x != null) {
                    String xid = x.getIdref();
                    String s = getIDSpace(xid);
                    if (treatMap.containsKey(s)) {
                        treatMap.get(s).expand(f, id, xid);
                    }
                }
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        if (!id.isEmpty()) {
            id = removeTrailingWS(id);
            if (id.contains(" ")) {
                warn("accepting bad xref with spaces:" + id);
            }
            Xref xref = new Xref(id);
            cl.addXref(xref);
            parseZeroOrMoreWs();
            if (stream.peekCharIs('"')) {
                stream.consume("\"");
                xref.setAnnotation(getParseUntilAdv("\""));
            }
            return true;
        }
        return false;
    }
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        id = id.trim();
        if (id.contains(" ")) {
            warn("accepting bad xref with spaces:<" + id + '>');
        }
        id = id.replaceAll(" +\\Z", "");
        @SuppressWarnings("null")
        Xref xref = new Xref(id);
        cl.addValue(xref);
        parseZeroOrMoreWs();
        if (stream.peekCharIs('"')) {
            stream.consume("\"");
            xref.setAnnotation(getParseUntilAdv("\""));
        }
        return true;
    }
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        Frame partOf = d2.getTypedefFrame("part_of");
        Collection<Clause> xrcs = partOf.getClauses(OboFormatTag.TAG_XREF);
        boolean okBfo = false;
        boolean okOboRel = false;
        for (Clause c : xrcs) {
            Xref value = c.getValue(Xref.class);
            if (value.getIdref().equals("BFO:0000050")) {
                okBfo = true;
            }
            if (value.getIdref().equals("OBO_REL:part_of")) {
                okOboRel = true;
            }
        }
        assertTrue(okBfo);
        assertTrue(okOboRel);
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        Clause defClause = frame.getClause(OboFormatTag.TAG_DEF);
        assertNotNull(defClause);
        Collection<Xref> xrefs = defClause.getXrefs();
        assertEquals(2, xrefs.size());
        Iterator<Xref> iterator = xrefs.iterator();
        Xref xref1 = iterator.next();
        assertEquals("RESID:AA0151", xref1.getIdref());
        String annotation = xref1.getAnnotation();
        assertEquals("variant", annotation);
        Xref xref2 = iterator.next();
        assertEquals("UniMod:148", xref2.getIdref());
        String original = readResource("db_xref_comments.obo");
        String renderedOboString = renderOboToString(obodoc);
        assertEquals(original, renderedOboString);
    }
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    }

    @SuppressWarnings("null")
    private static void writeXRefClause(@Nonnull Clause clause,
            @Nonnull BufferedWriter writer) throws IOException {
        Xref xref = clause.getValue(Xref.class);
        if (xref != null) {
            StringBuilder sb = new StringBuilder();
            sb.append(clause.getTag());
            sb.append(": ");
            String idref = xref.getIdref();
            int colonPos = idref.indexOf(':');
            if (colonPos > 0) {
                sb.append(escapeOboString(idref.substring(0, colonPos),
                        EscapeMode.xref));
                sb.append(':');
                sb.append(escapeOboString(idref.substring(colonPos + 1),
                        EscapeMode.xref));
            } else {
                sb.append(escapeOboString(idref, EscapeMode.xref));
            }
            String annotation = xref.getAnnotation();
            if (annotation != null) {
                sb.append(" \"");
                sb.append(escapeOboString(annotation, EscapeMode.quotes));
                sb.append('"');
            }
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        List<Xref> sortedXrefs = new ArrayList<>(xrefs);
        Collections.sort(sortedXrefs, XrefComparator.INSTANCE);
        sb.append(" [");
        Iterator<Xref> xrefsIterator = sortedXrefs.iterator();
        while (xrefsIterator.hasNext()) {
            Xref current = xrefsIterator.next();
            String idref = current.getIdref();
            int colonPos = idref.indexOf(':');
            if (colonPos > 0) {
                sb.append(escapeOboString(idref.substring(0, colonPos),
                        EscapeMode.xrefList));
                sb.append(':');
                sb.append(escapeOboString(idref.substring(colonPos + 1),
                        EscapeMode.xrefList));
            } else {
                sb.append(escapeOboString(idref, EscapeMode.xrefList));
            }
            String annotation = current.getAnnotation();
            if (annotation != null) {
                sb.append(' ');
                sb.append('"');
                sb.append(escapeOboString(annotation, EscapeMode.quotes));
                sb.append('"');
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Related Classes of org.obolibrary.oboformat.model.Xref

  • org.obolibrary.obo2owl.BFOROXrefTest
  • org.obolibrary.obo2owl.OWLAPIObo2Owl
  • org.obolibrary.obo2owl.OWLAPIOwl2Obo
  • org.obolibrary.oboformat.DbXrefCommentsTest
  • org.obolibrary.oboformat.parser.OBOFormatParser
  • org.obolibrary.oboformat.parser.XrefExpander
  • org.obolibrary.oboformat.writer.OBOFormatWriter
  • org.obolibrary.oboformat.writer.OBOFormatWriter$ClauseComparator
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