for (Iterator<Annotation> it = aJCas.getAnnotationIndex(t).iterator(); it.hasNext();) { EntityMention em = (EntityMention) it.next(); String specificType = em.getSpecificType(); JCoReSetAnnotationIndex<EntityMention> specificIndex = indexMap.get(specificType); if (null == specificIndex) { refEntity.setBegin(begin); refEntity.setEnd(end); refEntity.setSpecificType(entity.getSpecificType()); refEntity.setResourceEntryList(entity.getResourceEntryList()); refEntity.setConfidence(entity.getConfidence());
if (!StringUtils.isBlank(entity.getSpecificType())) specificType = entity.getSpecificType(); JCoReSetAnnotationIndex<EntityMention> set = overlapIndex.get(specificType); if (null == set) { final EntityMention entity = entityMap.get(entityString).iterator().next(); String specificType = "<null>"; if (!StringUtils.isBlank(entity.getSpecificType())) specificType = entity.getSpecificType(); JCoReSetAnnotationIndex<EntityMention> overlapSet = overlapIndex.get(specificType); refEntity.setSpecificType(entity.getSpecificType()); refEntity.setResourceEntryList(entity.getResourceEntryList()); refEntity.setConfidence(entity.getConfidence());
newEntityMention.setBegin(abbreviation.getBegin()); newEntityMention.setEnd(abbreviation.getEnd()); newEntityMention.setSpecificType(refEntityMention.getSpecificType()); newEntityMention.setResourceEntryList(refEntityMention.getResourceEntryList()); newEntityMention.setConfidence(refEntityMention.getConfidence()); newEntityMention.setBegin(fullform.getBegin()); newEntityMention.setEnd(fullform.getEnd()); newEntityMention.setSpecificType(refEntityMention.getSpecificType()); newEntityMention.setResourceEntryList(refEntityMention.getResourceEntryList()); newEntityMention.setConfidence(refEntityMention.getConfidence());