/* 
 *       Copyright 1991 Steven Smith at the Harvard Genome Lab.
 *       All rights reserved.
 */
#include "Flatio.c"

int Comp(a,b)
char a,b;
{
    static int CtoB[128]={
        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0x00,
        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
        0x01,0xe,0x02,0x0d,0,0,0x04,0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06,
        0x08,0x08,0x07,0,0x09,0xa,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,
        0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06,0x08,0x08,0x07,0,0x09,0x0a,
        0,0,0,0,0x00,0
    };

    return ((CtoB[a]) & (CtoB[b]));
}

int FindNext(target,offset,enzymes,numenzymes,match_len,color)
char *target,enzymes[][80];
int offset,numenzymes,*match_len,*color;
{
    int i,j,k,closest,len1,dif,flag = FALSE;
    closest = strlen(target);
    *match_len = 0;
    for(k=0;k<numenzymes;k++)
    {
        dif = (strlen(target)) - (len1 = strlen(enzymes[k])) +1;

        if(len1>0)
            for(flag = FALSE,j=offset;j<dif && flag == FALSE;j++)
            {
                flag = TRUE;
                for(i=0;i<len1 && flag;i++)
                {
                    flag = Comp(enzymes[k][i],target[i+j])?
                        TRUE:FALSE;
                }
            }
        if(j-1<closest)
        {
            closest = j-1;
            *color = k%6+1;
            *match_len = strlen(enzymes[k]);
        }
    }
    if(closest + *match_len < (int)strlen(target))
        return(closest);
    else
        return(-1);
}

int main(ac,av)
int ac;
char **av;
{
    struct data_format data[10000];
    FILE *file;
    int i,j,k,color,numseqs,numenzymes,nextpos,len;
    char enzymes[80][80],dummy[80];
    if(ac<3)
    {
        fprintf(stderr,"Usage: %s enzyme_file seq_file\n",av[0]);
        return -1;
    }
    file = fopen(av[2],"r");
    if(file == NULL)
        return -1;

    numseqs = ReadFlat(file,data,10000);

    file = fopen(av[1],"r");
    if(file == NULL)
        return -1;

    for(numenzymes = 0;
        fscanf(file,"%s %s",enzymes[numenzymes],dummy)>0;
        numenzymes++);

    for(i=0;i<numseqs;i++)
    {
/*
  if(numseqs>1)
*/
        printf("name:%s\n",data[i].name);
        printf("length:%zu\n",strlen(data[i].nuc));
        if(numseqs>1)
            printf("nodash:\n");
        printf("start:\n");
        for(j=0;j<data[i].length;)
        {
            for(;data[i].nuc[j] == '-' && j<data[i].length;)
            {
                printf("8\n");
                j++;
            }
            if((nextpos = FindNext(data[i].nuc,j,enzymes,numenzymes
                                   ,&len,&color)) != -1)
            {
                for(k=j;k<nextpos;k++)
                    printf("8\n");
                for(k=j+nextpos;k<j+nextpos+len;k++)
                    printf("%d\n",color);
                j=nextpos+len;
            }
            else
                for(;j<data[i].length;j++)
                    printf("8\n");
        }
    }
    return 0;
}