source: branches/lib/GDE/SUPPORT/sho_helix.c

#include "Flatio.c"
#define BLACK 8
#define RED 3
#define BLUE 6
#define YELLOW 1
#define AQUA 4

int match(a,b)
char a,b;
{
        char aa,bb;
        aa=a|32;
        bb=b|32;

        fprintf(stderr,"%c %c\n",aa,bb);

        if(a=='-' || a=='~')
        {
                if((b=='-') || (b=='~'))
                        return(BLACK);
                else
                        return(RED);
        }
        else if(aa=='a' && (bb=='t' || bb=='u'))
                return(BLUE);
        else if(bb=='a' && (aa=='t' || aa=='u'))
                return(BLUE);
        else if(bb=='c' && aa=='g' )
                return(BLUE);
        else if(bb=='g' && aa=='c' )
                return(BLUE);
        else if(aa=='g' && (bb=='t' || bb=='u'))
                return(AQUA);
        else if(bb=='g' && (aa=='t' || aa=='u'))
                return(AQUA);
        else return(YELLOW);
}


int main()
{
        struct data_format data[10000];
        int i,j,k,numseqs,mask = -1;
        int pair[20000],stack[20000],spt = 0;

        numseqs = ReadFlat(stdin,data,10000);
        if(numseqs == 0)
                return 1;
        for(j=0;j<numseqs;j++)
                if(data[j].type == '"')
                        mask = j;
        if(mask == -1)
                return 1;

        for(j=0;j<data[mask].length;j++)
        {
                if(data[mask].nuc[j] == '[')
                        stack[spt++] = j;
                else if(data[mask].nuc[j] == ']')
                {
                        i = stack[--spt];
                        pair[j] = i;
                        pair[i] = j;
                }
                else
                        pair[j] = -1;
        }

        for(j=0;j<numseqs;j++)
                if(j!=mask)
                {
                        printf("name:%s\nlength:%d\nstart:\n",
                                data[j].name,data[j].length);
                        i = MIN(data[mask].length,data[j].length);
                        for(k=0;k<i;k++)
                                if(pair[k] != -1)
                                        printf("%d\n",match(data[j].nuc[k],
                                                data[j].nuc[pair[k]]));
                                else
                                        printf("8\n");
                        for(k=0;k<data[j].length - data[mask].length;k++)
                                        printf("8\n");
                }
        return 0;
}