3-m.java

/* The Computer Language Benchmarks Game
 https://salsa.debian.org/benchmarksgame-team/benchmarksgame/

 contributed by James McIlree
 ByteString code thanks to Matthieu Bentot and The Anh Tran
 modified by Andy Fingerhut 
 */

import java.util.*;
import java.io.*;
import java.util.concurrent.*;

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

    static Map<ByteString, ByteString> createFragmentMap(byte[] sequence, int offset, int fragmentLength) {
        HashMap<ByteString, ByteString> map = new HashMap<ByteString, ByteString>();
        int lastIndex = sequence.length - fragmentLength + 1;
        ByteString key = new ByteString(fragmentLength);
        for (int index = offset; index < lastIndex; index += fragmentLength) {
            key.calculateHash(sequence, index);
            ByteString fragment = map.get(key);
            if (fragment != null) {
                fragment.count++;
            } else {
                map.put(key, key);
                key = new ByteString(fragmentLength);
            }
        }

        return map;
    }

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

    static String writeFrequencies(float totalCount, Map<ByteString, ByteString> frequencies) {
        SortedSet<ByteString> list = new TreeSet<ByteString>(frequencies.values());
        StringBuilder sb = new StringBuilder();
        for (ByteString k : list)
            sb.append(String.format("%s %.3f\n", k.toString().toUpperCase(), (float) (k.count) * 100.0f / totalCount));

        return sb.append('\n').toString();
    }

    static String writeCount(List<Future<Map<ByteString, ByteString>>> futures, String nucleotideFragment)
            throws Exception {
        ByteString key = new ByteString(nucleotideFragment.length());
        key.calculateHash(nucleotideFragment.getBytes(), 0);

        int count = 0;
        for (Future<Map<ByteString, ByteString>> future : futures) {
            ByteString temp = future.get().get(key);
            if (temp != null)
                count += temp.count;
        }

        return count + "\t" + nucleotideFragment.toUpperCase() + '\n';
    }

    public static void main(String[] args) throws Exception {
        String fileName = args.length > 0 ? args[0] : "25000_in";
        String line;
        BufferedReader in = new BufferedReader(new FileReader(fileName));
        while ((line = in.readLine()) != null) {
            if (line.startsWith(">THREE"))
                break;
        }

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        byte bytes[] = new byte[100];
        while ((line = in.readLine()) != null) {
            if (line.length() > bytes.length)
                bytes = new byte[line.length()];

            int i;
            for (i = 0; i < line.length(); i++)
                bytes[i] = (byte) line.charAt(i);
            baos.write(bytes, 0, i);
        }

        byte[] sequence = baos.toByteArray();

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

        StringBuilder sb = new StringBuilder();

        sb.append(writeFrequencies(sequence.length, futures.get(0).get()));
        sb.append(writeFrequencies(sequence.length - 1, sumTwoMaps(futures.get(1).get(), futures.get(2).get())));

        String[] nucleotideFragments = { "ggt", "ggta", "ggtatt", "ggtattttaatt", "ggtattttaatttatagt" };
        for (String nucleotideFragment : nucleotideFragments) {
            sb.append(writeCount(futures, nucleotideFragment));
        }

        System.out.print(sb.toString());
        in.close();
    }

    static final class ByteString implements Comparable<ByteString> {
        public int hash, count = 1;
        public final byte bytes[];

        public ByteString(int size) {
            bytes = new byte[size];
        }

        public void calculateHash(byte k[], int offset) {
            int temp = 0;
            for (int i = 0; i < bytes.length; i++) {
                byte b = k[offset + i];
                bytes[i] = b;
                temp = temp * 31 + b;
            }
            hash = temp;
        }

        public int hashCode() {
            return hash;
        }

        public boolean equals(Object obj) {
            return Arrays.equals(bytes, ((ByteString) obj).bytes);
        }

        public int compareTo(ByteString other) {
            if (other.count != count) {
                return other.count - count;
            } else {
                // Without this case, if there are two or more strings
                // with exactly the same count in a Map, then the
                // TreeSet constructor called in writeFrequencies will
                // only add the first one, and the rest will not
                // appear in the output. Also this is required to
                // satisfy the rules of the k-nucleotide problem.
                return toString().compareTo(other.toString());
            }
        }

        public String toString() {
            return new String(bytes);
        }
    }
}