对字符串进行反补。

/*

 * Copyright (c) 2014. Real Time Genomics Limited.

 *

 * Use of this source code is bound by the Real Time Genomics Limited Software Licence Agreement

 * for Academic Non-commercial Research Purposes only.

 *

 * If you did not receive a license accompanying this file, a copy must first be obtained by email

 * from support@realtimegenomics.com.  On downloading, using and/or continuing to use this source

 * code you accept the terms of that license agreement and any amendments to those terms that may

 * be made from time to time by Real Time Genomics Limited.

 */

//package com.nowjava;
/* 
*来 自
 n o w j a   v  a . c o m - 时  代  Java
*/


public class Main {

    /**

     * Take reverse complement of a string.

     * @param seq to be reverse complemented.

     * @return the reversed sequence.

     */

    public static String reverseComplement(final String seq) {

        final StringBuilder sb = new StringBuilder();

        for (int i = seq.length() - 1; i >= 0; i--) {

            final char c = seq.charAt(i);

            switch (c) {

            case 'a':

                sb.append('t');

                break;

            case 'A':

                sb.append('T');

                break;

            case 'c':

                sb.append('g');

                break;

            case 'C'://n o w j a   v  a . c o m - 时  代  Java 提 供

                sb.append('G');

                break;

            case 'g':

                sb.append('c');

                break;

            case 'G':

                sb.append('C');

                break;

            case 't':

                sb.append('a');

                break;

            case 'T':

                sb.append('A');

                break;

            case '-':

                break;

            default: // n

                sb.append(c);

                break;

            }

        }

        return sb.toString();

    }


    /**

     * Transform a human-readable DNA sequence into the reverse complemented version, uppercase.

     * @param src Eg. {'a','c','g','t','n'} will become {'N', 'A', 'C', 'G', 'T'}.

     * @param dest destination byte array

     * @param length length to convert

     */

    public static void reverseComplement(byte[] src, byte[] dest, int length) {

        for (int k = 0; k < length; k++) {

            switch (src[k]) {

            case (byte) 'a':

            case (byte) 'A':

                dest[length - 1 - k] = 'T';

                break;

            case (byte) 'c':

            case (byte) 'C':

                dest[length - 1 - k] = 'G';

                break;