序列比对（23）最长公共子字符串

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define MAXSEQ 1000

void strUpper(char *s);
void printAlign(int** a, const int i, const int j, char* s, char* r, int n);
void align(char *s, char *r);

int main() {
    char s[MAXSEQ];
    char r[MAXSEQ];
    printf("The 1st seq: ");
    scanf("%s", s);
    printf("The 2nd seq: ");
    scanf("%s", r);
    align(s, r);
    return 0;
}

void strUpper(char *s) {
    while (*s != '\0') {
        if (*s >= 'a' && *s <= 'z') {
            *s -= 32;
        }
        s++;
    }
}

void printAlign(int** a, const int i, const int j, char* s, char* r, int n) {
    int k;
    int p = a[i - n][j - n];
    if (p == 0) {   // 到值为0的矩阵单元就结束
        printf("start and end position of common seq in seq1: %d %d\n", i - n + 1, i);
        printf("start and end position of common seq in seq2: %d %d\n", j - n + 1, j);
        for (k = 0; k < n; k++)
            printf("%c", s[i - n + k]);
        printf("\n");
        for (k = 0; k < n; k++)
            printf("%c", r[j - n + k]);
        printf("\n\n");
        return;
    }
    printAlign(a, i, j, s, r, n + 1);
}

void align(char *s, char *r) {
    int i, j;
    int m = strlen(s);
    int n = strlen(r);
    int **aUnit;
    int max;
    // 初始化
    if ((aUnit = (int**) malloc(sizeof(int*) * (m + 1))) == NULL) {
        fputs("Error: Out of space!\n", stderr);
        exit(1);
    }
    for (i = 0; i <= m; i++) {
        if ((aUnit[i] = (int*) malloc(sizeof(int) * (n + 1))) == NULL) {
            fputs("Error: Out of space!\n", stderr);
            exit(1);     
        }
    }
    for (i = 0; i <= m; i++)
        aUnit[i][0] = 0;
    for (j = 1; j <= n; j++)
        aUnit[0][j] = 0;
    // 将字符串都变成大写
    strUpper(s);
    strUpper(r);
    // 动态规划算法计算得分矩阵每个单元的分值
    for (i = 1; i <= m; i++)
        for (j = 1; j <= n; j++)
            aUnit[i][j] = s[i - 1] == r[j - 1] ? aUnit[i - 1][j - 1] + 1 : 0;
/*
    // 打印得分矩阵
    for (i = 0; i <= m; i++) {
        for (j = 0; j <= n; j++)
            printf("%d ", aUnit[i][j]);
        printf("\n");
    }
*/
    for (i = 1, max = 0; i <= m; i++)
        for (j = 1; j <= n; j++)
            if (aUnit[i][j] > max)
                max = aUnit[i][j];
    printf("max score: %d\n", max);
    // 打印最优比对结果，如果有多个，全部打印
    // 递归法
    if (max == 0) {
        fputs("No common sub str found.\n", stdout);
    } else {
        for (i = 1; i <= m; i++)
            for (j = 1; j <= n; j++)
                if (aUnit[i][j] == max)
                    printAlign(aUnit, i, j, s, r, 0);
    }
    for (i = 0; i <= m; i++)
        free(aUnit[i]);
    free(aUnit);
}