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import java.util.Arrays;

/**

* BWT编码

*/

public class BWTCode {

public static void main(String[] args) {

//String str = "GATCAAATGGGGGATCGATC";

String str = "GATCAAATGGGGGATCGATCGATCGATCCCCCATTTGATC";

System.out.println("输入的字符串是：" + str);

String enCodeStr = enCode(str);

System.out.println("编码后的字符串是：" + enCodeStr);

System.out.println("解码后的字符串是：" + deCode(enCodeStr));

}

public static String enCode(String line) {

String str = line + "&";

int len = str.length();

char[] charArray = str.toCharArray();

char[][] ch = new char[len][len];

for (int i = 0; i < len; i++) {

char[] c_tmp = charArray.clone();

for (int j = 0; j < len; j++) {

ch[i][j] = c_tmp[j];

if (j <= len - 2) charArray[j + 1] = c_tmp[j];

}

charArray[0] = c_tmp[len - 1];

}

String[] strings = new String[len];

for (int i = 0; i < len; i++) {

StringBuffer chline = new StringBuffer();

for (char c : ch[i]) {

chline.append(c);

}

strings[i] = chline.toString();

}

Arrays.sort(strings);

StringBuffer sBuffer = new StringBuffer();

for (String s : strings) {

sBuffer.append(s.substring(len - 1, len));

}

return sBuffer.toString();

}

public static String deCode(String str) {

int len = str.length();

String[] strArr = new String[len];

for (int i = 0; i < len; i++) {

strArr[i] = str.substring(i, i + 1) + ":" + i;

}

Arrays.sort(strArr);

StringBuffer sb = new StringBuffer();

int num = 0;

int corr = Integer.parseInt(strArr[0].split(":")[1]);

while (num < len - 1) {

sb.append(strArr[corr].split(":")[0]);

corr = Integer.parseInt(strArr[corr].split(":")[1]);

num++;

}

return sb.toString();

}

}