source code
/* The Computer Language Benchmarks Game
* https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
*
* 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:
64-bit Ubuntu quad core
openjdk 14 2020-03-17
OpenJDK Runtime Environment (build 14+36-1461)
OpenJDK 64-Bit Server VM (build 14+36-1461, mixed mode, sharing)
Tue, 05 May 2020 01:48:27 GMT
MAKE:
mv knucleotide.java-4.java knucleotide.java
/opt/src/openjdk-14/bin/javac -d . -cp .:/opt/src/java-libs/fastutil-8.1.0.jar knucleotide.java
3.23s to complete and log all make actions
COMMAND LINE:
/opt/src/openjdk-14/bin/java -cp .:/opt/src/java-libs/fastutil-8.1.0.jar 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