Class knucleotide

benchmark/bench/knucleotide.java:11–125

import java.util.concurrent.*;

public class knucleotide {
    String sequence;
    int count = 1;

    knucleotide(String sequence) {
        this.sequence = sequence;
    }

    static ArrayList<Callable< Map<String, knucleotide> > > createFragmentTasks(final String sequence, int[] fragmentLengths) {
        ArrayList<Callable<Map<String, knucleotide>>> tasks = new ArrayList<Callable<Map<String, knucleotide>>>();
        for (int fragmentLength : fragmentLengths) {
            for (int index=0; index<fragmentLength; index++) {
                final int offset = index;
                final int finalFragmentLength = fragmentLength;
                tasks.add(new Callable<Map<String, knucleotide>>() {
                    public Map<String, knucleotide> call() {
                    return createFragmentMap(sequence, offset, finalFragmentLength);
                    }
                });
            }
        }
        return tasks;
    }

    static Map<String, knucleotide> createFragmentMap(String sequence, int offset, int fragmentLength) {
        HashMap<String, knucleotide> map = new HashMap<String, knucleotide>();
        int lastIndex = sequence.length() - fragmentLength + 1;
        for (int index=offset; index<lastIndex; index+=fragmentLength) {
            String temp = sequence.substring(index, index + fragmentLength);
            knucleotide fragment = (knucleotide)map.get(temp);
            if (fragment != null)
            fragment.count++;
            else
            map.put(temp, new knucleotide(temp));
        }

        return map;
    }

    // Destructive!
    static Map<String, knucleotide> sumTwoMaps(Map<String, knucleotide> map1, Map<String, knucleotide> map2) {
        for (Map.Entry<String, knucleotide> entry : map2.entrySet()) {
            knucleotide sum = (knucleotide)map1.get(entry.getKey());
            if (sum != null)
            sum.count += entry.getValue().count;
            else
            map1.put(entry.getKey(), entry.getValue());
        }
        return map1;
    }

    static String writeFrequencies(Map<String, knucleotide> frequencies) {
        ArrayList<knucleotide> list = new ArrayList<knucleotide>(frequencies.size());
        int sum = 0;
        for (knucleotide fragment : frequencies.values()) {
            list.add(fragment);
            sum += fragment.count;
        }