Method main

benchmark/bench/knucleotide.java:97–123

(String[] args)

    }

    public static void main (String[] args) throws Exception {
        String line;
        BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
        while ((line = in.readLine()) != null) {
            if (line.startsWith(">THREE")) break;
        }

        StringBuilder sbuilder = new StringBuilder();
        while ((line = in.readLine()) != null) {
            sbuilder.append(line);
        }

        ExecutorService pool = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
        int[] fragmentLengths = { 1, 2, 3, 4, 6, 12, 18 };
        List<Future<Map<String, knucleotide>>> futures = pool.invokeAll(createFragmentTasks(sbuilder.toString(), fragmentLengths));
        pool.shutdown();

        // Print the length 1 & 2 counts. We know the offsets of the tasks, so we can cheat.
        System.out.println(writeFrequencies(futures.get(0).get()));
        System.out.println(writeFrequencies(sumTwoMaps(futures.get(1).get(), futures.get(2).get())));

        System.out.println(writeCount(futures, "ggt"));
        System.out.println(writeCount(futures, "ggta"));
        System.out.println(writeCount(futures, "ggtatt"));
        System.out.println(writeCount(futures, "ggtattttaatt"));
        System.out.println(writeCount(futures, "ggtattttaatttatagt"));
    }

}