# include "stdio.h"
# include "stdlib.h"//stdlib 头文件即standard library标准库头文件。stdlib.h里面定义了五种类型、一些宏和通用工具函数。
# include "time.h"# define N 60        void PreIndex();//建立索引文本,目录文本
void DeepInfo1();//关键信息提取
void Search();//进行查找
long DeepInfo2();
int main()
{//PreIndex();//DeepInfo();
    Search();printf("结束");return 0;
}void PreIndex()
{FILE * fpIndex, * fpCatalog, * fpsource1, * fpsource2;//定义四个指针，分别指向目标文件和两个附件个指针，分别指向目标文件和两个附件fpCatalog = fopen("Catalog.txt","w");fpIndex = fopen("Index.txt","w");//目标文件指针指向目标文件if ((fpsource1=fopen("solexa_100_170_1.fa","r")) == NULL){printf("Can't open the solexa_100_170_1.fa!\n");getchar();exit(-1);}//if做出判断的同时也指明了指针的指向if ((fpsource2=fopen("solexa_100_170_2.fa","r")) == NULL){printf("Can't open the solexa_100_170_2.fa!\n");getchar();exit(-1);}int i;char ch;char str[101];//VC中是不能在中间定义变量的，所以这个代码必须在c99标准下编译for (i=0; i<500000; i++)//通过循环从第一个附件中读取50万个数据
    {while ((ch=fgetc(fpsource1)) && (ch<'A' || ch>'T'))putc(ch,fpCatalog);fputc(ch,fpIndex);fgets(str,101,fpsource1);fputs(str,fpIndex);}        //while (ch=fgetc(fpsource1) && (ch<'A' || ch>'T'));这样是不对的，为什么说不清//这一句好好理解，即读取的字符ASCII码不是ATCG时就不执行操作（注意while后面直接加分号表示不执行操作）//执行while时包含了一个先对ch赋值的操作，每执行while文件位置指针都会后移一个，注意理解for (i=0; i<500000; i++)//通过循环从第一个附件中读取50万个数据
    {while ((ch=fgetc(fpsource2)) && (ch<'A' || ch>'T'))putc(ch,fpCatalog);fputc(ch,fpIndex);fgets(str,101,fpsource2);fputs(str,fpIndex);}fclose(fpCatalog);fclose(fpIndex);fclose(fpsource1);fclose(fpsource2);}void DeepInfo1()
{FILE * fp,* fp0;char ch;int i = 0,j = 0;fp = fopen("Catalog.txt", "r");fp0 = fopen("DeepCatalog.txt", "w");while ((ch = fgetc(fp)) && ch != EOF){if (ch == '0')//1
        {ch = fgetc(fp);if (ch == '0')//2
            {ch = fgetc(fp);if(ch == '0')//3
                {ch = fgetc(fp);if (ch == '0')//4
                    {ch = fgetc(fp);if(ch == '0')//5ch = fgetc(fp);if(ch == '0')//6ch = fgetc(fp);if(ch == '0')//7
                                {ch = fgetc(fp);ch = fgetc(fp);do{fputc(ch,fp0);ch = fgetc(fp);}while(ch != ' ');fputc('\n',fp0);}}}}}}fclose(fp);}
void Search()
{FILE * fpIndex = fopen("Index.txt","r");FILE * fpDeepInfo = fopen("DeepInfo.txt","r");int i = 0,j = -1,n = 0,m = 0, y = -1,v = 0,x = 0,key = 0,q = 0,w = 1;char s[105],p[N];int loc[100];//loc位location位置数组
printf("请输入长度为%d的模式串\n", N);scanf("%s", p);for(i=0; i<1000000; i++){fgets(s,105    ,fpIndex);while(q<(100-N+1)){if(s[n] == p[m]){n++;m++;if (m == N){n = n - N + 1;m = 0;q = n;j = n;y++;loc[y] = n;}}else{n = n - m +1;q = n;m = 0;}}n = 0;q = 0;m = 0;if(j != -1){if(i>=500000)w = 2;key = DeepInfo2(i);printf(">read_170_%d_%d random_genome_10000000 %d 100\n", i+1, w, key);//1还是2，加判断printf("{");for(v=0;v<(y+1);v++)printf("%d, ", loc[v]);printf("\b\b}\n");y = -1;}j = -1;    }fclose(fpIndex);fclose(fpDeepInfo);
}long DeepInfo2(int i)
{long key,j,a;FILE * fp;fp = fopen("DeepCatalog.txt","r");a = i;for (j=0;j<a;j++)fscanf(fp,"%*ld",&key);fscanf(fp,"%ld",&key);fclose(fp);return key;
}//void IndexArray()
//{}
//void Search()
//{}