/**
* Parse a bufferedReader and process GFF3 record
*
* @param bReader the Reader
* @throws java.io.IOException if an error occurs reading GFF
* @throws ObjectStoreException if an error occurs storing items
*/
public void parse(BufferedReader bReader) throws IOException, ObjectStoreException {
GFF3Record record;
long start, now, opCount;
opCount = 0;
start = System.currentTimeMillis();
boolean duplicates = false;
Set<String> processedIds = new HashSet<String>();
Set<String> duplicatedIds = new HashSet<String>();
for (Iterator<?> i = GFF3Parser.parse(bReader); i.hasNext(); ) {
record = (GFF3Record) i.next();
// we only care about dupes if we are NOT creating locations
if (processedIds.contains(record.getId()) && dontCreateLocations) {
duplicates = true;
duplicatedIds.add(record.getId());
} else {
if (record.getId() != null) {
processedIds.add(record.getId());
}
}
if (!duplicates) {
process(record);
}
opCount++;
if (opCount % 1000 == 0) {
now = System.currentTimeMillis();
LOG.info("processed " + opCount + " lines --took " + (now - start) + " ms");
start = System.currentTimeMillis();
}
}
if (duplicates) {
LOG.error("Duplicated IDs in GFF file: " + duplicatedIds);
throw new IllegalArgumentException("Duplicated IDs in GFF file: " + duplicatedIds);
}
}
