/** Performs name finding on the given cas object. */
public final void process(CAS cas) {
if (isRemoveExistingAnnotations) {
final AnnotationComboIterator sentenceNameCombo =
new AnnotationComboIterator(cas, mSentenceType, mNameType);
List<AnnotationFS> removeAnnotations = new LinkedList<AnnotationFS>();
for (AnnotationIteratorPair annotationIteratorPair : sentenceNameCombo) {
for (AnnotationFS nameAnnotation : annotationIteratorPair.getSubIterator()) {
removeAnnotations.add(nameAnnotation);
}
}
for (AnnotationFS annotation : removeAnnotations) {
cas.removeFsFromIndexes(annotation);
}
}
final AnnotationComboIterator sentenceTokenCombo =
new AnnotationComboIterator(cas, mSentenceType, mTokenType);
for (AnnotationIteratorPair annotationIteratorPair : sentenceTokenCombo) {
final List<AnnotationFS> sentenceTokenAnnotationList = new LinkedList<AnnotationFS>();
final List<String> sentenceTokenList = new LinkedList<String>();
for (AnnotationFS tokenAnnotation : annotationIteratorPair.getSubIterator()) {
sentenceTokenAnnotationList.add(tokenAnnotation);
sentenceTokenList.add(tokenAnnotation.getCoveredText());
}
Span[] names =
find(cas, (String[]) sentenceTokenList.toArray(new String[sentenceTokenList.size()]));
AnnotationFS nameAnnotations[] = new AnnotationFS[names.length];
for (int i = 0; i < names.length; i++) {
int startIndex =
((AnnotationFS) sentenceTokenAnnotationList.get(names[i].getStart())).getBegin();
int endIndex =
((AnnotationFS) sentenceTokenAnnotationList.get(names[i].getEnd() - 1)).getEnd();
nameAnnotations[i] = cas.createAnnotation(mNameType, startIndex, endIndex);
cas.getIndexRepository().addFS(nameAnnotations[i]);
}
postProcessAnnotations(names, nameAnnotations);
}
documentDone(cas);
}
/**
* Removes all annotations of type removeAnnotationType which are contained by annotations of type
* containerAnnotationType.
*
* @param cas
* @param containerAnnotationType
* @param removeAnnotationType
*/
public static void removeAnnotations(
CAS cas, AnnotationFS containerAnnotation, Type removeAnnotationType) {
FSIndex<AnnotationFS> allRemoveAnnotations = cas.getAnnotationIndex(removeAnnotationType);
ContainingConstraint containingConstraint = new ContainingConstraint(containerAnnotation);
Iterator<AnnotationFS> containingTokens =
cas.createFilteredIterator(allRemoveAnnotations.iterator(), containingConstraint);
Collection<AnnotationFS> removeAnnotations = new LinkedList<AnnotationFS>();
while (containingTokens.hasNext()) {
removeAnnotations.add(containingTokens.next());
}
for (Iterator<AnnotationFS> it = removeAnnotations.iterator(); it.hasNext(); ) {
cas.removeFsFromIndexes(it.next());
}
}
