Iterator wtIter = FSUtil.getAnnotationsInSpanIterator(
jcas, WordToken.type, begin, end);
int cnt=0;
while(wtIter.hasNext()) {
WordToken wt = (WordToken) wtIter.next();
if(ignoreWords.contains(wt.getCoveredText().toLowerCase())) continue;
boolean isNE = false;
for(IdentifiedAnnotation n : neLst) {
if(n.getBegin()<=wt.getBegin() && n.getEnd()>=wt.getEnd()) {
isNE = true;
break;
}
}
if(isNE) continue;