最长公共子序列LCS

最长公共子序列(LCS)算法
 输入：随机生成两条字符序列，长度最少为10000。
 输出：求解时间，最长公共子序列及其长度。

 

算法思想：

设X=<x1,x2,x3,…,xm>和Y=<y1,y2,y3,…,yn>为两个序列，并设Z=<z1,z2,z3,…zk>为X和Y的任意一个LCS

1. 如果xm=yn=zk，那么Zk-1是Xm-1和Yn-1的一个LCS

2. 如果xm不等于yn,那么zk不等于xm蕴含Z是Xm-1和Y的一个LCS

3. 如果xm不等于yn,那么zk不等于yn蕴含Z是X和Yn-1的一个LCS

 

因此基于算法导论上的LCS算法给予以下几方面的优化：

1. 去掉用来构造最优解的数组，节省了O(mn)的存储空间

2. 将二维数组的类型从int改为short

3. 将LCS_Print()程序由递归改为非递归，解决了数据量过大时会出现的堆栈溢出。

 

实现代码如下：

#include  <stdlib.h>
#include  <stdio.h>
#include  <string.h>
#include<time.h>


#define MAXSIZE  10000
short C[MAXSIZE][MAXSIZE] = { 0 };

void LCS_Length(char *S1, char *S2){

	int i, j;
	int len1 = strlen(S1), len2 = strlen(S2);
	for (i = 0; i <len2; i++)
		C[i][0] = 0;   //S2 column
	for (i = 0; i <len1; i++)
		C[0][i] = 0;  //S1 row 

	for (i = 1; i < len2; i++)
		for (j = 1; j < len1; j++){
			if (S1[j] == S2[i]){
				C[i][j] = C[i - 1][j - 1] + 1;
			}
			else if (C[i - 1][j] >= C[i][j - 1]){
				C[i][j] = C[i - 1][j];
			}
			else{
				C[i][j] = C[i][j - 1];
			}
		}
}

/*
void LCS_Print(char *S2, int i, char *S1, int j){
	if (i == 0 || j == 0) return;
	if (S1[j] == S2[i]){
		LCS_Print(S2, i - 1,S1, j - 1);
		printf("%c", S1[j]);
	}
	else if (C[i - 1][j] >= C[i][j - 1]){
		LCS_Print(S2, i - 1,S1, j);
	}
	else
		LCS_Print(S2, i,S1, j - 1);
}
*/

    
void reverse(char *S){
	int i = 0, j = strlen(S) - 1;
	int temp;
	for (; i <= j; i++, j--){
		temp = S[i];
		S[i] = S[j];
		S[j] = temp;
	}
}


void LCS_Print(char *S2, int i, char *S1, int j){
	char S[MAXSIZE] = { ' ' };
	int len = 0;
	while (i != 0 && j != 0) {
		if (S1[j] == S2[i]){
			S[len++] = S1[j];
			i--; 
			j--;
		}
		else if (C[i - 1][j] >= C[i][j - 1])
			i--;
		else
			j--;
	}
	S[len] = '\0';
	reverse(S);
	printf("%s\nLCS Length:%d\n",S,strlen(S));
}



void main(){
	int  j, len1, len2;
	clock_t start;
	clock_t duringtime;
	//char S1[] = " ACCGGTCGAGTGCGCGGAAGCCGGCCGAA";//"BDCABA";
	//char S2[] = " GTCGTTCGGAATGCCGTTGCTCTGTAAA";

	char S1[MAXSIZE] = { '0' };
	char S2[MAXSIZE] = { '0' };

	for (j = 1; j <MAXSIZE; j++){
		S1[j] = ('A' + rand() % 25);
	}
	S1[9999] = '\0';
	for (j = 1; j <MAXSIZE; j++){
		S2[j] = ('A' + rand() % 25);
	}
	S2[9999] = '\0';
	start = clock();
	LCS_Length(S1, S2);
	len1 = strlen(S1)-1;
	len2 = strlen(S2)-1;
	//printf("S1:%s\n", S1);
	//printf("S2:%s\n", S2);
	printf("LCS:");
	LCS_Print(S2, len2, S1,len1);
	duringtime = clock() - start;
	printf("Time:");
	printf("%f ms\n", (double)(duringtime));
}