/** @generated * @param jcas JCas to which this Feature Structure belongs * @param begin offset to the begin spot in the SofA * @param end offset to the end spot in the SofA */ public EventMention(JCas jcas, int begin, int end) { super(jcas); setBegin(begin); setEnd(end); readObject(); }
EventMention newGoldEventMention = new EventMention(goldView, oldSystemEventMention.getBegin(), oldSystemEventMention.getEnd()); newGoldEventMention.setDiscoveryTechnique(oldSystemEventMention.getDiscoveryTechnique()); newGoldEventMention.setUncertainty(oldSystemEventMention.getUncertainty()); newGoldEventMention.setConditional(oldSystemEventMention.getConditional()); newGoldEventMention.setGeneric(oldSystemEventMention.getGeneric()); newGoldEventMention.setPolarity(oldSystemEventMention.getPolarity()); newGoldEventMention.setSubject(oldSystemEventMention.getSubject()); newGoldEventMention.setHistoryOf(oldSystemEventMention.getHistoryOf()); newGoldEventMention.setConfidence(oldSystemEventMention.getConfidence()); newGoldEventMention.setTypeID(oldSystemEventMention.getTypeID()); newGoldEventMention.addToIndexes();
EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end); addIdentifiedAnnotationFeatures( annotation, EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end); addIdentifiedAnnotationFeatures( annotation, EventMention eventMention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end); eventMention.setConfidence(1.0f); eventMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION); event.setMentions(new FSArray(jCas, 1)); event.setMentions(0, eventMention); eventMention.setEvent(event); eventMention.addToIndexes(); idAnnotationMap.put(annotation.id, eventMention);
/** * Does more than a typical reader - also creates an IdentifiedAnnotation * and a DocumentID annotation */ @Override public void getNext(CAS aCAS) throws IOException, CollectionException { JCas jCas; try { jCas = aCAS.getJCas(); } catch(CASException e){ throw new CollectionException(e); } NegExAnnotation a = list.get(i); i++; jCas.setDocumentText(a.sentenceText); DocumentID documentID = new DocumentID(jCas); documentID.setDocumentID("doc" + a.lineNumber); documentID.addToIndexes(); EventMention ia = new EventMention(jCas); ia.setBegin(Integer.parseInt(a.begin)); ia.setEnd(Integer.parseInt(a.end)); if (!skipReadingValuesJustReadText) ia.setPolarity(Integer.parseInt(a.polarity)); ia.addToIndexes(); }
int end = charOffset + m.group(1).length(); EventMention mention = new EventMention(jcas, charOffset, end); mention.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT); mention.setConditional(CONST.NE_CONDITIONAL_FALSE); mention.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT); mention.setGeneric(CONST.NE_GENERIC_FALSE); mention.setSubject(CONST.ATTR_SUBJECT_PATIENT); mention.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT); }else if(m.group(7).equals("hypothetical")){ mention.setConditional(CONST.NE_CONDITIONAL_TRUE); }else if(m.group(7).equals("possible")){ mention.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT); }else if(m.group(7).equals("associated_with_someone_else")){ mention.setSubject(CONST.ATTR_SUBJECT_FAMILY_MEMBER); // the most common non-patient case }else if(m.group(7).equals("conditional")){ // no good mapping. mention.addToIndexes();
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { Collection<EventMention> mentions = JCasUtil.select(jCas, EventMention.class); for (EventMention mention : Lists.newArrayList(mentions)) { int begin = mention.getBegin(); int end = mention.getEnd(); int typeID = mention.getTypeID(); List<EventMention> subMentions = JCasUtil.selectCovered(jCas, EventMention.class, mention); for (EventMention subMention : subMentions) { if (subMention.getBegin() > begin || subMention.getEnd() < end) { if (subMention.getTypeID() == typeID) { String message = String.format("removed %s inside %s", format(subMention), format(mention)); this.getContext().getLogger().log(Level.WARNING, message); subMention.removeFromIndexes(); } } } } } }
/** Internal - constructor used by generator * @generated * @param addr low level Feature Structure reference * @param type the type of this Feature Structure */ public EventMention(int addr, TOP_Type type) { super(addr, type); readObject(); }
ConllDependencyNode eventHead = getNominalHeadNode(jcas, event); if(eventHead == head){ if(markableEvent == null || (event.getEnd()-event.getBegin()) > (markableEvent.getEnd()-markableEvent.getBegin())){ markableEvent = event; neg = markableEvent.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT; feats.add(new Feature("SemEnvNegation", neg));
error("Illegal negative span", id); EventMention event = new EventMention(entCas, begin, end); event.addToIndexes();
private static String getDocTimeRelForArg(JCas jCas, IdentifiedAnnotation arg){ String dtr = "NA"; // find EventMentions and grab their event properties ConllDependencyNode node = DependencyUtility.getNominalHeadNode(jCas, arg); if(node != null){ List<EventMention> events = JCasUtil.selectCovered(jCas, EventMention.class, node); for(EventMention event : events){ if(event.getClass().getSimpleName().equals("EventMention")){ if(event.getEvent() != null && event.getEvent().getProperties() != null && event.getEvent().getProperties().getDocTimeRel() != null){ dtr = event.getEvent().getProperties().getDocTimeRel(); } } } } return dtr; } }
|| type==CONST.NE_TYPE_ID_ANATOMICAL_SITE ) { eMention = new EventMention(initView, first.start, last.end); } else { eMention = new IdentifiedAnnotation(initView, first.start, last.end);
final Event event = createEvent( jCas, extensions ); if ( event != null ) { ((EventMention) annotation).setEvent( event );
EventMention newGoldEventMention = new EventMention(goldView, oldSystemEventMention.getBegin(), oldSystemEventMention.getEnd()); newGoldEventMention.setDiscoveryTechnique(oldSystemEventMention.getDiscoveryTechnique()); newGoldEventMention.setUncertainty(oldSystemEventMention.getUncertainty()); newGoldEventMention.setConditional(oldSystemEventMention.getConditional()); newGoldEventMention.setGeneric(oldSystemEventMention.getGeneric()); newGoldEventMention.setPolarity(oldSystemEventMention.getPolarity()); newGoldEventMention.setSubject(oldSystemEventMention.getSubject()); newGoldEventMention.setHistoryOf(oldSystemEventMention.getHistoryOf()); newGoldEventMention.setConfidence(oldSystemEventMention.getConfidence()); newGoldEventMention.setTypeID(oldSystemEventMention.getTypeID()); newGoldEventMention.addToIndexes();
EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end); addIdentifiedAnnotationFeatures( annotation, EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end); addIdentifiedAnnotationFeatures( annotation, EventMention eventMention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end); eventMention.setConfidence(1.0f); eventMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION); event.setMentions(new FSArray(jCas, 1)); event.setMentions(0, eventMention); eventMention.setEvent(event); eventMention.addToIndexes(); idAnnotationMap.put(annotation.id, eventMention);
/** * Does more than a typical reader - also creates an IdentifiedAnnotation * and a DocumentID annotation */ @Override public void getNext(CAS aCAS) throws IOException, CollectionException { JCas jCas; try { jCas = aCAS.getJCas(); } catch(CASException e){ throw new CollectionException(e); } NegExAnnotation a = list.get(i); i++; jCas.setDocumentText(a.sentenceText); DocumentID documentID = new DocumentID(jCas); documentID.setDocumentID("doc" + a.lineNumber); documentID.addToIndexes(); EventMention ia = new EventMention(jCas); ia.setBegin(Integer.parseInt(a.begin)); ia.setEnd(Integer.parseInt(a.end)); if (!skipReadingValuesJustReadText) ia.setPolarity(Integer.parseInt(a.polarity)); ia.addToIndexes(); }
int end = charOffset + m.group(1).length(); EventMention mention = new EventMention(jcas, charOffset, end); mention.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT); mention.setConditional(CONST.NE_CONDITIONAL_FALSE); mention.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT); mention.setGeneric(CONST.NE_GENERIC_FALSE); mention.setSubject(CONST.ATTR_SUBJECT_PATIENT); mention.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT); }else if(m.group(7).equals("hypothetical")){ mention.setConditional(CONST.NE_CONDITIONAL_TRUE); }else if(m.group(7).equals("possible")){ mention.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT); }else if(m.group(7).equals("associated_with_someone_else")){ mention.setSubject(CONST.ATTR_SUBJECT_FAMILY_MEMBER); // the most common non-patient case }else if(m.group(7).equals("conditional")){ // no good mapping. mention.addToIndexes();
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { Collection<EventMention> mentions = JCasUtil.select(jCas, EventMention.class); for (EventMention mention : Lists.newArrayList(mentions)) { int begin = mention.getBegin(); int end = mention.getEnd(); int typeID = mention.getTypeID(); List<EventMention> subMentions = JCasUtil.selectCovered(jCas, EventMention.class, mention); for (EventMention subMention : subMentions) { if (subMention.getBegin() > begin || subMention.getEnd() < end) { if (subMention.getTypeID() == typeID) { String message = String.format("removed %s inside %s", format(subMention), format(mention)); this.getContext().getLogger().log(Level.WARNING, message); subMention.removeFromIndexes(); } } } } } }
/** Internal - constructor used by generator * @generated * @param addr low level Feature Structure reference * @param type the type of this Feature Structure */ public EventMention(int addr, TOP_Type type) { super(addr, type); readObject(); }