source: branches/help/GDE/SUPPORT/Restriction.c

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


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]);
                exit(-1);
        }
        file = fopen(av[2],"r");
        if(file == NULL)
                exit(-1);

        numseqs = ReadFlat(file,data,10000);

        file = fopen(av[1],"r");
        if(file == NULL)
                exit(-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");
                }
        }
        exit(0);
}


FindNext(target,offset,enzymes,numenzymes,match_len,color)
char *target,enzymes[][80];
int 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 < strlen(target))
                return(closest);
        else
                return(-1);
}

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
        };

        static int BtoC[128] =
        {
        '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
        '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
        '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
        '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
        '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
        '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
        '-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
        '~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
        };


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