changed
void get_seq_scores(double seq_scores[MAX_CLASS_NUMBER], Sequence sequence, 
                       double dimer_like[MAXSEQLEN][POSNUM+1],
		       double trimer_like[MAXSEQLEN][POSNUM+1],
                       double bound, double weighted_avg)
to
void get_seq_scores(double seq_scores[MAX_CLASS_NUMBER], Sequence sequence, 
                       double dimer_like[MAXSEQLEN][POSNUM+1],
		       double trimer_like[MAXSEQLEN][POSNUM+1],
                       double bound)


changed 
        if (weighted_avg) weight= dimer_like[i][7] + trimer_like[i][7];
        else weight = 1;
to weight= dimer_like[i][7] + trimer_like[i][7];