revcomp.java

package shootout.revcomp;

import java.io.*;

public class revcomp {
	static final byte[] cmp = new byte[128];

	static {
		for (int i = 0; i < cmp.length; i++) cmp[i] = (byte) i;
		cmp['t'] = cmp['T'] = 'A';
		cmp['a'] = cmp['A'] = 'T';
		cmp['g'] = cmp['G'] = 'C';
		cmp['c'] = cmp['C'] = 'G';
		cmp['v'] = cmp['V'] = 'B';
		cmp['h'] = cmp['H'] = 'D';
		cmp['r'] = cmp['R'] = 'Y';
		cmp['m'] = cmp['M'] = 'K';
		cmp['y'] = cmp['Y'] = 'R';
		cmp['k'] = cmp['K'] = 'M';
		cmp['b'] = cmp['B'] = 'V';
		cmp['d'] = cmp['D'] = 'H';
		cmp['u'] = cmp['U'] = 'A';
	}

	static class ReversibleByteArray extends java.io.ByteArrayOutputStream {
		void reverse() throws Exception {
			if (count > 0) {
				int begin = 0, end = count - 1;
				while (buf[begin++] != '\n') ;
				while (begin <= end) {
					if (buf[begin] == '\n') begin++;
					if (buf[end] == '\n') end--;
					if (begin <= end) {
						byte tmp = buf[begin];
						buf[begin++] = cmp[buf[end]];
						buf[end--] = cmp[tmp];
					}
				}
				System.out.write(buf, 0, count);
			}
		}
	}

	public static void main(String[] args) throws Exception {
		long start = System.currentTimeMillis();
		byte[] line = new byte[82];
		int read;
		ReversibleByteArray buf = new ReversibleByteArray();
		while ((read = System.in.read(line)) != -1) {
			int i = 0, last = 0;
			while (i < read) {
				if (line[i] == '>') {
					buf.write(line, last, i - last);
					buf.reverse();
					buf.reset();
					last = i;
				}
				i++;
			}
			buf.write(line, last, read - last);
		}
		buf.reverse();
		long total = System.currentTimeMillis() - start;
		System.out.println("[Revcomp-Java Benchmark Result: " + total + "]");
	}
}