source: trunk/GDE/SUPPORT/findall.c

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

int CompIUP(a,b)
char a,b;
{
        static int matr[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,
        0x08,0x08,0x07,0x09,0x00,0xa,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,
        0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06,0x08,0x08,0x07,0x09,0x00,0x0a,
        0,0,0,0,0x00,0
        };


        int testa,testb;

        if(a&32 != b&32)
                return(FALSE);

        testa = matr[(int)a];
        testb = matr[(int)b];
        return(testa&testb);
}

int main(ac,av)
int ac;
char **av;
{
        struct data_format data[10000];
        int Match = 2,Mismatch = 8;
        int i,j,k,numseqs,mis,Case = 32;
        int slen,pcnt,pos;
        int UT = FALSE;
        char c;
        if(ac < 3)
        {
                fprintf(stderr,
"usage: %s search_string %%mismatch [-case] [-match color] [-mismatch color]\n",
                av[0]);
                fprintf(stderr,"                [-u=t]\n");
                return 0;
        }
        for (j=3;j<ac;j++)
        {
                if(strcmp("-case",av[j]) == 0)
                        Case = 0;
                if(strcmp("-match",av[j]) == 0)
                        sscanf(av[j+1],"%d",&Match);
                if(strcmp("-u=t",av[j]) == 0)
                        UT = TRUE;
                if(strcmp("-mismatch",av[j]) == 0)
                        sscanf(av[j+1],"%d",&Mismatch);
        }
        numseqs = ReadFlat(stdin,data,10000);

        slen = strlen(av[1]);
        sscanf(av[2],"%d",&pcnt);
        pcnt *= slen;
        pcnt /= 100;

        if(UT)
        {
            int av1Len = strlen(av[1]);
            for(j=0;j<=av1Len;j++)
            {
                if(av[1][j] == 't')
                    av[1][j] = 'u';
                if(av[1][j] == 'T')
                    av[1][j] = 'U';
            }
        }

        for(i=0;i<numseqs;i++)
        {
                if(UT)
                        for(j=0;data[i].nuc[j]!='\0';j++)
                        {
                                if(data[i].nuc[j] == 't') 
                                        data[i].nuc[j] = 'u';
                                else if(data[i].nuc[j] == 'T') 
                                        data[i].nuc[j] = 'U';
                        }
                printf("name:%s\n",data[i].name);
                printf("length:%zu\n",strlen(data[i].nuc));
                printf("start:\n");
                for(j=0;j<data[i].length;j++)
                {
                        mis = 0;
                        for(k=0,pos=j;k<slen && pos<data[i].length;k++,pos++)
                        {
                                c = data[i].nuc[pos];
                                for(;(c == ' ' || c == '-' || c == '~') &&
                                        pos < data[i].length;)
                                        c = data[i].nuc[++pos];
                                c |= Case;

                                if(data[i].type == '#')
                                {
                                    if(CompIUP(c,(av[1][k]|Case)) == FALSE)
                                        mis++;
                                }
                                else
                                {
                                    if(c!=(av[1][k]|Case))
                                        mis++;
                                }
                        }
                        if(k == slen && mis<=pcnt)
                        {
                                for(k=j;k<pos;k++)
                                        printf("%d\n",Match);
                                j = pos-1;
                        }
                        else
                                printf("%d\n",Mismatch);
                }
        }
        return 0;
}