The Computer Language
Benchmarks Game

k-nucleotide Java #4 program

source code

/* The Computer Language Benchmarks Game
 * http://benchmarksgame.alioth.debian.org/
 *
 * contributed by Daryl Griffith 
 */

import java.io.Closeable;
import java.io.IOException;
import java.io.InputStream;
import java.nio.ByteBuffer;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;

public class knucleotide {

    static final Map<Key, Value> MAP = new HashMap<>();
    static final int[] SEQUENCES1 = {2, 1};
    static final int[] SEQUENCES2 = {18, 12, 6, 4, 3};
    static final String[] SPICIFIC_SEQUENCES = new String[]{"GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"};
    static final int LINE_LENGTH = 60;
    static final int EOF = -1;
    static byte[] nucleotides;

    public static void main(String[] args) {
        {
            byte[] temp = new byte[LINE_LENGTH];
            byte[] buffer = new byte[125_000_000];
            byte[] species = ">TH".getBytes();
            int n;
            int i;

            try (LineInputStream in = new LineInputStream(System.in)) {
outer:
                for (;;) {
                    n = in.readLine(temp);
                    if (n == EOF) {
                        return;
                    }
                    if (n != LINE_LENGTH) {
                        for (i = 0; i < species.length; i++) {
                            if (temp[i] != species[i]) {
                                continue outer;
                            }
                        }
                        break;
                    }
                }
                i = 0;
                for (;;) {
                    n = in.readLine(temp);
                    if (n == EOF) {
                        break;
                    }
                    for (int j = 0; j < n; i++, j++) {
                        buffer[i] = translate(temp[j]);
                    }
                }
                if (i == buffer.length) {
                    nucleotides = buffer;
                } else {
                    nucleotides = new byte[i];
                    System.arraycopy(buffer, 0, nucleotides, 0, i);
                }
            } catch (IOException e) {

            }
        }
        countSequences(SEQUENCES1);
        {
            List<Entry<Key, Value>> sequence1 = new ArrayList<>();
            List<Entry<Key, Value>> sequence2 = new ArrayList<>();

            for (Entry<Key, Value> entry : MAP.entrySet()) {
                switch (Long.numberOfLeadingZeros(entry.getKey().key)) {
                    case 61:
                        sequence1.add(entry);
                        break;
                    case 59:
                        sequence2.add(entry);
                }
            }
            printSequence(sequence1);
            printSequence(sequence2);
        }
        countSequences(SEQUENCES2);
        {
            Key key = new Key();

            for (String sequence : SPICIFIC_SEQUENCES) {
                key.setHash(sequence);
                System.out.print(MAP.get(key).count);
                System.out.print('\t');
                System.out.println(sequence);
            }
        }
    }
        
    static byte translate(byte b) {
        return (byte) ((b >> 1) & 3);
    }

    static void countSequences(int[] sequences) {
        for (int sequence : sequences) {
            updateHashtable(sequence);
        }
    }

    static void updateHashtable(int sequence) {
        int sequenceTop = nucleotides.length - sequence + 1;
        Key key = new Key();
        Value value;
        
        for (int i = 0; i < sequenceTop; i++) {
            key.setHash(i, sequence);
            value = MAP.get(key);
            if (value == null) {
                value = new Value();
                value.count = 1;
                MAP.put(key, value);
                key = new Key();
            } else {
                value.count++;
            }
        }
    }

    static void printSequence(List<Entry<Key, Value>> sequence) {
        int sum = 0;

        Collections.sort(sequence, new Comparator<Entry<Key, Value>>() {

            @Override
            public int compare(Entry<Key, Value> entry1, Entry<Key, Value> entry2) {
                if (entry2.getValue().count != entry1.getValue().count) {
                    return entry2.getValue().count - entry1.getValue().count;
                }
                return entry1.getKey().toString().compareTo(entry2.getKey().toString());
            }
        });
        for (Entry<Key, Value> entry : sequence) {
            sum += entry.getValue().count;
        }
        for (Entry<Key, Value> entry : sequence) {
            System.out.format("%s %.3f\n", entry.getKey(), entry.getValue().count * 100f / sum);
        }
        System.out.println();
    }

    static class LineInputStream implements Closeable {

        private static final int LF = 10;
        private final ByteBuffer buffer = ByteBuffer.allocate(8192);
        private final InputStream in;

        public LineInputStream(InputStream in) {
            this.in = in;
            buffer.limit(buffer.position());
        }

        public int readLine(byte[] b) throws IOException {
            for (int end = buffer.position(); end < buffer.limit(); end++) {
                if (buffer.get(end) == LF) {
                    if (end - buffer.position() == LINE_LENGTH) {
                        buffer.get(b);
                        buffer.position(buffer.position() + 1);
                        return LINE_LENGTH;
                    } else {
                        int size = end - buffer.position();

                        buffer.get(b, 0, size);
                        buffer.position(buffer.position() + 1);
                        return size;
                    }
                }
            }
            buffer.compact();
            int n = in.read(buffer.array(), buffer.position(), buffer.remaining());

            if (n == EOF) {
                buffer.flip();
                if (buffer.hasRemaining()) {
                    int size = buffer.remaining();

                    buffer.get(b, 0, size);
                    return size;
                } else {
                    return EOF;
                }
            } else {
                buffer.position(buffer.position() + n);
                buffer.flip();
            }
            for (int end = buffer.position(); end < buffer.limit(); end++) {
                if (buffer.get(end) == LF) {
                    if (end - buffer.position() == LINE_LENGTH) {
                        buffer.get(b);
                        buffer.position(buffer.position() + 1);
                        return LINE_LENGTH;
                    } else {
                        int size = end - buffer.position();

                        buffer.get(b, 0, size);
                        buffer.position(buffer.position() + 1);
                        return size;
                    }
                }
            }
            return EOF;
        }

        @Override
        public void close() throws IOException {
            in.close();
        }
    }

    static class Key {

        long key;

        void setHash(int offset, int length) {
            key = 1;
            for (int i = offset + length - 1; i >= offset; i--) {
                key = (key << 2) | nucleotides[i];
            }
        }

        void setHash(String species) {
            key = 1;
            for (int i = species.length() - 1; i >= 0; i--) {
                key = (key << 2) | translate((byte) species.charAt(i));
            }
        }

        @Override
        public int hashCode() {
            return (int) key;
        }

        @Override
        public boolean equals(Object obj) {
            final Key other = (Key) obj;

            return key == other.key;
        }

        @Override
        public String toString() {
            char[] name = new char[(63 - Long.numberOfLeadingZeros(key)) / 2];
            long temp = key;

            for (int i = 0; temp > 1; temp >>= 2, i++) {
                name[i] = (char) (((temp & 3) << 1) | 'A');
                if (name[i] == 'E') {
                    name[i] = 'T';
                }
            }
            return new String(name);
        }
    }

    static class Value {

        int count;
    }
}
    

notes, command-line, and program output

NOTES:
32-bit Ubuntu one core
java version "1.8.0_92"
Java(TM) SE Runtime Environment (build 1.8.0_92-b14)
Java HotSpot(TM) Server VM (build 25.92-b14, mixed mode)


Mon, 09 May 2016 02:40:45 GMT

MAKE:
mv knucleotide.java-4.java knucleotide.java
/usr/local/src/jdk1.8.0_92/bin/javac knucleotide.java
0.81s to complete and log all make actions

COMMAND LINE:
/usr/local/src/jdk1.8.0_92/bin/java -Xmx2048m -server -XX:+TieredCompilation -XX:+AggressiveOpts knucleotide 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT