/**
* Rename annotation
*
* @param outputAS output annotation set
* @param oldType old annotation name
* @param newType new annotation name
*/
private void renameAnnotations(AnnotationSet outputAS, String oldType, String newType) {
AnnotationSet tmpAnatomyAS = outputAS.get(oldType);
for (Annotation tmpAnn : tmpAnatomyAS) {
Long startOffset = tmpAnn.getStartNode().getOffset();
Long endOffset = tmpAnn.getEndNode().getOffset();
AnnotationSet existingAS = outputAS.getCovering(newType, startOffset, endOffset);
// If we've already got an annotation of the same name in the same place, don't add a new one
// just delete the old one
if (existingAS.isEmpty()) {
FeatureMap tmpFm = tmpAnn.getFeatures();
FeatureMap fm = Factory.newFeatureMap();
fm.putAll(tmpFm);
try {
outputAS.add(startOffset, endOffset, newType, fm);
outputAS.remove(tmpAnn);
} catch (InvalidOffsetException ie) {
// shouldn't happen
}
} else {
outputAS.remove(tmpAnn);
}
}
}
/**
* @param inputAS input annotation set
* @param outputAS output annotation set
* @param term String matched
* @param startOffset match start offset
* @param endOffset match end offset
*/
private void addLookup(
AnnotationSet inputAS,
AnnotationSet outputAS,
String term,
String outputASType,
Long startOffset,
Long endOffset,
boolean useNounChunk) {
if (useNounChunk && nounChunkType != null && !nounChunkType.isEmpty()) {
AnnotationSet nounChunkAS = inputAS.getCovering(nounChunkType, startOffset, endOffset);
if (!nounChunkAS.isEmpty()) {
startOffset = nounChunkAS.firstNode().getOffset();
endOffset = nounChunkAS.lastNode().getOffset();
}
}
try {
AnnotationSet diseaseAS = inputAS.get(outputASType, startOffset, endOffset);
if (diseaseAS.isEmpty()) {
FeatureMap fm = Factory.newFeatureMap();
fm.put("match", term);
outputAS.add(startOffset, endOffset, outputASType, fm);
} else {
Annotation disease = diseaseAS.iterator().next();
FeatureMap fm = disease.getFeatures();
String meta = (String) fm.get("match");
if (meta != null) {
meta = meta + " " + term;
}
fm.put("match", meta);
}
} catch (InvalidOffsetException ie) {
// shouldn't happen
gate.util.Err.println(ie);
}
}