public void setDefault(OBOVocabulary tag, String value) { defaults.put(tag.getIRI(), value); }
public void setDefault(OBOVocabulary tag, String value) { defaults.put(tag.getIRI(), value); }
public void setDefault(OBOVocabulary tag, String value) { defaults.put(tag.getIRI(), value); }
public void addPair(OBOVocabulary tag, String value) { addPair(tag.getIRI(), value); }
public void addPair(OBOVocabulary tag, String value) { addPair(tag.getIRI(), value); }
public void addPair(OBOVocabulary tag, String value) { addPair(tag.getIRI(), value); }
private void loadBuiltinURIs() { for (OBOVocabulary v : OBOVocabulary.values()) { uriCache.put(v.getName(), v.getIRI()); } }
private void loadBuiltinURIs() { for (OBOVocabulary v : OBOVocabulary.values()) { uriCache.put(v.getName(), v.getIRI()); } }
public void setPair(OBOVocabulary key, String value) { knownTVPs.remove(key.getName()); addPair(key.getIRI(), value); }
private void loadBuiltinURIs() { for (OBOVocabulary v : OBOVocabulary.values()) { uriCache.put(v.getName(), v.getIRI()); } }
public void setPair(OBOVocabulary key, String value) { knownTVPs.remove(key.getName()); addPair(key.getIRI(), value); }
public void setPair(OBOVocabulary key, String value) { knownTVPs.remove(key.getName()); addPair(key.getIRI(), value); }
public void write(Writer writer) { this.writer = writer; // write tags out in order for (OBOVocabulary tag : vocab) { Set<String> values = knownTVPs.get(tag.getName()); if (values == null) { String def = defaults.get(tag.getIRI()); if (def != null) { values = Collections.singleton(def); } } if (values != null) { for (String value : values) { writeTagValuePair(tag, value); } } } // write additional tags in no specified order for (String unknownTag : unknownTVPs.keySet()) { for (String value : unknownTVPs.get(unknownTag)) { writeTagValuePair(unknownTag, value); } } }
public OBOConsumer(OWLOntology ontology, OWLOntologyLoaderConfiguration configuration, IRI baseIRI) { this.configuration = configuration; owlOntologyManager = ontology.getOWLOntologyManager(); this.ontology = ontology; intersectionOfOperands = new HashSet<OWLClassExpression>(); unionOfOperands = new HashSet<OWLClassExpression>(); uriCache = new HashMap<String, IRI>(); for (OBOVocabulary v : OBOVocabulary.values()) { tagIRICache.put(v.getName(), v.getIRI()); } ontologyTagValue = getDefaultOntologyTagValue(baseIRI); loadBuiltinURIs(); setupTagHandlers(); }
@SuppressWarnings("deprecation") public OBOConsumer(OWLOntology ontology, OWLOntologyLoaderConfiguration configuration, IRI baseIRI) { this.configuration = configuration; this.owlOntologyManager = ontology.getOWLOntologyManager(); this.ontology = ontology; intersectionOfOperands = new HashSet<OWLClassExpression>(); unionOfOperands = new HashSet<OWLClassExpression>(); uriCache = new HashMap<String, IRI>(); for (OBOVocabulary v : OBOVocabulary.values()) { tagIRICache.put(v.getName(), v.getIRI()); } this.ontologyTagValue = getDefaultOntologyTagValue(baseIRI); loadBuiltinURIs(); setupTagHandlers(); }
public void addPair(IRI tag, String value) { boolean found = false; for (OBOVocabulary obo : vocab) { if (tag.equals(obo.getIRI())) { addPair(obo.getName(), value, knownTVPs); found = true; break; } } if (!found) { final String name = iriSFP.getShortForm(tag); addPair(name, value, unknownTVPs); } }
public void addPair(IRI tag, String value) { boolean found = false; for (OBOVocabulary obo : vocab) { if (tag.equals(obo.getIRI())) { addPair(obo.getName(), value, knownTVPs); found = true; break; } } if (!found) { final String name = iriSFP.getShortForm(tag); addPair(name, value, unknownTVPs); } }
public void addPair(IRI tag, String value) { boolean found = false; for (OBOVocabulary obo : vocab) { if (tag.equals(obo.getIRI())) { addPair(obo.getName(), value, knownTVPs); found = true; break; } } if (!found) { final String name = iriSFP.getShortForm(tag); addPair(name, value, unknownTVPs); } }
@Override public void handle(String currentId, String value, String qualifierBlock, String comment) { IRI subject = getConsumer().getCurrentEntity().getIRI(); IRI annotationPropertyIRI = OBOVocabulary.ALT_ID.getIRI(); OWLAnnotationProperty property = getDataFactory().getOWLAnnotationProperty(annotationPropertyIRI); IRI object = getIRIFromOBOId(value); OWLAnnotationAssertionAxiom ax = getDataFactory().getOWLAnnotationAssertionAxiom(property, subject, object); applyChange(new AddAxiom(getOntology(), ax)); } }
public void handle(String currentId, String value, String qualifierBlock, String comment) { IRI subject = getConsumer().getCurrentEntity().getIRI(); IRI annotationPropertyIRI = OBOVocabulary.ALT_ID.getIRI(); OWLAnnotationProperty property = getDataFactory().getOWLAnnotationProperty(annotationPropertyIRI); IRI object = getIRIFromOBOId(value); OWLAnnotationAssertionAxiom ax = getDataFactory().getOWLAnnotationAssertionAxiom(property, subject, object); applyChange(new AddAxiom(getOntology(), ax)); } }