revcomp.java

/*
 * The Computer Language Benchmarks Game
 * http://shootout.alioth.debian.org/
 * contributed by Anthony Donnefort
 * redone by Enotus 2010-11-20
 */

import java.io.*;

public final class revcomp {

    static final byte[] map=new byte[128];
        static{
        String[] mm={"ACBDGHK\nMNSRUTWVYacbdghkmnsrutwvy","TGVHCDM\nKNSYAAWBRTGVHCDMKNSYAAWBR"};
        for(int i=0;i<mm[0].length();i++) map[mm[0].charAt(i)]=(byte)mm[1].charAt(i);
    } 

    static void reverse(byte[] buf,int begin,int end){
        while(true){
            byte bb=buf[begin];if(bb=='\n') bb=buf[++begin];
            byte be=buf[end];if(be=='\n') be=buf[--end];
            if(begin>end) break;
            buf[begin++]=map[be];
            buf[end--]=map[bb];
        }
    }
      
    public static void main(String[] args) throws IOException{
        final byte[] buf=new byte[System.in.available()];
        System.in.read(buf);

        for(int i=0;i<buf.length;){
            while(buf[i++]!='\n');
            int data=i; while(i<buf.length && buf[i++]!='>');
            reverse(buf,data,i-2);
        }

        System.out.write(buf);
    }
}