neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG ); neAnnot.setBegin( neBegin ); neAnnot.setEnd( neEnd );
eMention.setTypeID(Mapper.getEntityTypeId(entityTypes.get(mentionId))); eMention.setId(identifiedAnnotationId++); eMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG ); neAnnot.setBegin( neBegin ); neAnnot.setEnd( neEnd );
annotation.setTypeID( cTakesSemantic ); annotation.setBegin( spanCuis.getKey().getStart() ); annotation.setEnd( spanCuis.getKey().getEnd() );
annotation.setTypeID( cTakesSemantic ); annotation.setBegin( spanCuis.getKey().getStart() ); annotation.setEnd( spanCuis.getKey().getEnd() );
eMention.setTypeID(Mapper.getEntityTypeId(entityTypes.get(mentionId))); eMention.setId(identifiedAnnotationId++); eMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
Map<String, TOP> idAnnotationMap, List<DelayedFeature> delayedFeatures) { mention.setTypeID(typeID); mention.setConfidence(1.0f); mention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
neAnnot = new EntityMention( jcas ); neAnnot.setTypeID( conceptKey ); neAnnot.setBegin( neBegin ); neAnnot.setEnd( neEnd );
Map<String, TOP> idAnnotationMap, List<DelayedFeature> delayedFeatures) { mention.setTypeID(typeID); mention.setConfidence(1.0f); mention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
Map<String, TOP> idAnnotationMap, List<DelayedFeature> delayedFeatures) { mention.setTypeID(typeID); mention.setConfidence(1.0f); mention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
neAnnot = new EntityMention( jcas ); neAnnot.setTypeID( conceptKey ); neAnnot.setBegin( neBegin ); neAnnot.setEnd( neEnd );
Map<String, TOP> idAnnotationMap, List<DelayedFeature> delayedFeatures) { mention.setTypeID(typeID); mention.setConfidence(1.0f); mention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
neAnnot.setDiscoveryTechnique( CONST.NE_DISCOVERY_TECH_DICT_LOOKUP ); neAnnot.setOntologyConceptArr( ocArr ); neAnnot.setTypeID( typeId ); neAnnot.addToIndexes();
neAnnot.setDiscoveryTechnique( CONST.NE_DISCOVERY_TECH_DICT_LOOKUP ); neAnnot.setOntologyConceptArr( ocArr ); neAnnot.setTypeID( typeId ); neAnnot.addToIndexes();
/** * * @param goldAnnotation * @param jcas */ private static void copyAnnotation(Annotation goldAnnotation, JCas jcas) { Annotation newAnno; if (goldAnnotation instanceof IdentifiedAnnotation) { IdentifiedAnnotation ia = new IdentifiedAnnotation(jcas); ia.setConditional(((IdentifiedAnnotation) goldAnnotation).getConditional()); ia.setConfidence(((IdentifiedAnnotation) goldAnnotation).getConfidence()); ia.setDiscoveryTechnique(((IdentifiedAnnotation)goldAnnotation).getDiscoveryTechnique()); ia.setGeneric(((IdentifiedAnnotation) goldAnnotation).getGeneric()); ia.setHistoryOf(((IdentifiedAnnotation) goldAnnotation).getHistoryOf()); ia.setPolarity(((IdentifiedAnnotation) goldAnnotation).getPolarity()); ia.setSegmentID(((IdentifiedAnnotation) goldAnnotation).getSegmentID()); ia.setSentenceID(((IdentifiedAnnotation) goldAnnotation).getSentenceID()); ia.setSubject(((IdentifiedAnnotation) goldAnnotation).getSubject()); ia.setTypeID(((IdentifiedAnnotation) goldAnnotation).getTypeID()); ia.setUncertainty(((IdentifiedAnnotation) goldAnnotation).getUncertainty()); newAnno = ia; } else { throw new RuntimeException("Unexpected class of object " + goldAnnotation.getClass()); } newAnno.setBegin(goldAnnotation.getBegin()); newAnno.setEnd(goldAnnotation.getEnd()); newAnno.addToIndexes(); }
/** * * @param goldAnnotation * @param jcas */ private static void copyAnnotation(Annotation goldAnnotation, JCas jcas) { Annotation newAnno; if (goldAnnotation instanceof IdentifiedAnnotation) { IdentifiedAnnotation ia = new IdentifiedAnnotation(jcas); ia.setConditional(((IdentifiedAnnotation) goldAnnotation).getConditional()); ia.setConfidence(((IdentifiedAnnotation) goldAnnotation).getConfidence()); ia.setDiscoveryTechnique(((IdentifiedAnnotation)goldAnnotation).getDiscoveryTechnique()); ia.setGeneric(((IdentifiedAnnotation) goldAnnotation).getGeneric()); ia.setHistoryOf(((IdentifiedAnnotation) goldAnnotation).getHistoryOf()); ia.setPolarity(((IdentifiedAnnotation) goldAnnotation).getPolarity()); ia.setSegmentID(((IdentifiedAnnotation) goldAnnotation).getSegmentID()); ia.setSentenceID(((IdentifiedAnnotation) goldAnnotation).getSentenceID()); ia.setSubject(((IdentifiedAnnotation) goldAnnotation).getSubject()); ia.setTypeID(((IdentifiedAnnotation) goldAnnotation).getTypeID()); ia.setUncertainty(((IdentifiedAnnotation) goldAnnotation).getUncertainty()); newAnno = ia; } else { throw new RuntimeException("Unexpected class of object " + goldAnnotation.getClass()); } newAnno.setBegin(goldAnnotation.getBegin()); newAnno.setEnd(goldAnnotation.getEnd()); newAnno.addToIndexes(); }
annotation.setTypeID( group.getCode() );
mention.setSentenceID(original.getSentenceID()); mention.setSubject(original.getSubject()); mention.setTypeID(original.getTypeID()); mention.setUncertainty(original.getUncertainty()); mention.setHistoryOf(original.getHistoryOf());