if (format == null) {
format = CmdOptions.DEFAULT_FORMAT;
}
ClassifierFactory factory = ClassifierFactory.getFactory(gene);
Classifier aClassifier = factory.createClassifier();
SeqReader parser = new SequenceReader(new File(inputFile));
BufferedWriter wt = new BufferedWriter(new FileWriter(outFile));
Sequence pSeq = null;
try {
while ((pSeq = parser.readNextSequence()) != null) {
try {
ClassificationResult result = aClassifier.classify(new ClassifierSequence(pSeq), min_bootstrap_words);
wt.write(ClassificationResultFormatter.getOutput(result, format));
} catch (ShortSequenceException e) {