public static void main(final String[] argv) throws IOException {
Set<String> args = new HashSet<String>(Arrays.asList(argv));
if (args.size() < 1) {
throw new RuntimeException(
"\r\nYou must specify a file name for input.\n"
+ "filename \n ----------------------------\n"
+ "Run with -d or --debug for debug output");
} else {
final Evaluate evaluate = new Evaluate(args);
final List<String> testFiles = new LinkedList<String>();
final boolean noCaching = args.contains("--nocache");
for (String arg : args) {
if (!arg.startsWith("-")) {
logger.info("Adding test dataset: " + arg);
testFiles.add(arg);
}
}
for (final String testSet : testFiles) {
logger.info("Using " + testSet + " tests");
evaluate.initializeHMMs(args);
final Iterator<PairHMM> pairHMMIterator = evaluate.pairHMM.iterator();
while (pairHMMIterator.hasNext()) {
final PairHMM hmm = pairHMMIterator.next();
final String hmmName = hmm.getClass().getSimpleName();
final String[] testSplit = testSet.split("/"); // get rid of the file path (if any)
final String testName =
testSplit[testSplit.length - 1].split("\\.")[0]; // get rid of the file extension
logger.info("Running " + hmmName);
evaluate.runTests(hmm, createIteratorFor(testSet), hmmName, testName, noCaching);
pairHMMIterator.remove();
}
logger.info("Finished all HMMs for " + testSet + " tests");
}
}
}
