// TODO
} else if ("generic_class".equals(annotation.type)) {
// TODO: there's currently no Generic in the type system
boolean value = booleanSlots.remove("generic_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("severity_class".equals(annotation.type)) {
Severity severity = new Severity(jCas);
severity.setValue(stringSlots.remove("severity_normalization"));
severity.addToIndexes();
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(severity);
idAnnotationMap.put(annotation.id, modifier);
} else if ("conditional_class".equals(annotation.type)) {
// TODO: there's currently no Conditional in the type system
boolean value = booleanSlots.remove("conditional_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("course_class".equals(annotation.type)) {
Course course = new Course(jCas);
course.setValue(stringSlots.remove("course_normalization"));
course.addToIndexes();
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(course);
idAnnotationMap.put(annotation.id, modifier);
} else if ("uncertainty_indicator_class".equals(annotation.type)) {
// TODO: there's currently no Uncertainty in the type system
String value = stringSlots.remove("uncertainty_indicator_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("distal_or_proximal".equals(annotation.type)) {
// TODO: there's currently no Distal or Proximal in the type system
String value = stringSlots.remove("distal_or_proximal_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("Person".equals(annotation.type)) {
// TODO: there's currently no Subject in the type system
String value = stringSlots.remove("subject_normalization_CU");
// TODO: what does a code mean on a Person?
String code = stringSlots.remove("associatedCode");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("body_side_class".equals(annotation.type)) {
BodySide bodySide = new BodySide(jCas);
bodySide.setValue(stringSlots.remove("body_side_normalization"));
bodySide.addToIndexes();
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(bodySide);
idAnnotationMap.put(annotation.id, modifier);
} else if ("negation_indicator_class".equals(annotation.type)) {
// TODO: there's currently no Negation in the type system
String value = stringSlots.remove("negation_indicator_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("historyOf_indicator_class".equals(annotation.type)) {
// TODO: there's currently no HistoryOf in the type system
String value = stringSlots.remove("historyOf_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("superior_or_inferior".equals(annotation.type)) {
// TODO: there's currently no Superior or Inferior in the type system
String value = stringSlots.remove("superior_or_inferior_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("medial_or_lateral".equals(annotation.type)) {
// TODO: there's currently no Medial or Lateral in the type system
String value = stringSlots.remove("medial_or_lateral_normalization");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("Route".equals(annotation.type)) {
// TODO: there's currently no Route in the type system
String value = stringSlots.remove("route_values");
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if ("Clinical_attribute".equals(annotation.type)) {
// TODO: what does this even mean?
Modifier modifier = new Modifier(jCas, coveringSpan.begin, coveringSpan.end);
// modifier.setNormalizedForm(...);
idAnnotationMap.put(annotation.id, modifier);
} else if (eventRelationTypes.contains(annotation.type)) {
// store the ALINK information for later, once all annotations are in the CAS