std_calculation_funcs.c

马尔科夫模型的java版本实现

  
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) / prf_column_length;
    }
  }
}

void add_to_E_picasso(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
		      int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;

  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share);
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) / prf_column_length;
    }
  }
}

void add_to_E_picasso_sym(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
		      int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;

  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share);
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) / prf_column_length;
    }
  }
}

void add_to_E_sjolander_score(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
			      int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;


  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share);
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) / prf_column_length;
    }
  }
}

void add_to_E_sjolander_reversed_score(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
				       int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;
  
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) / prf_column_length;
    }
  }
}

void add_to_E_dot_product_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
				 int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;

  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) / prf_column_length;
    }
  }
}

void add_to_E_dot_product_picasso_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
					 int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;

  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) / prf_column_length;
    }
  }
}

void add_to_E_picasso_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
				 int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;

  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) / prf_column_length;
    }
  }
}

void add_to_E_picasso_sym_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
				 int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;

  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) / prf_column_length;
    }
  }
}

void add_to_E_sjolander_score_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
				     int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;
  
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) / prf_column_length;
    }
  }
}

void add_to_E_sjolander_reversed_score_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
					      int k, int a_size, int normalize)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length;
  
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences);
      
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);
    }
    prf_column_length = sqrt(prf_column_length);
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) / prf_column_length;
    }
  }
}

void add_to_E_subst_mtx_product(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
			  int k, int a_size, int normalize, double *subst_mtx)
{
  int a_index, a_index2;
  double prf_column_length;
  double subst_mtx_row_length;
  
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      for(a_index2 = 0; a_index2 < a_size; a_index2++) {
	*(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	  (double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) *
	  *(subst_mtx + get_mtx_index(a_index, a_index2, a_size));
      }
    }
  }
  else {
    printf("Error: no normalizing in subst_mtx_product, yet...\n");
    exit(0);
  }

}
void add_to_E_subst_mtx_product_nr_occ(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
				       int k, int a_size, int normalize, double *subst_mtx)
{
  int a_index, a_index2;
  double prf_column_length;
  double subst_mtx_row_length;
  
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      for(a_index2 = 0; a_index2 < a_size; a_index2++) {
	*(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	  (double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->nr_occurences) *
	  *(subst_mtx + get_mtx_index(a_index, a_index2, a_size));
      }
    }
  }
  else {
    printf("Error: no normalizing in subst_mtx_product, yet...\n");
    exit(0);
  }

}

void add_to_E_subst_mtx_dot_product(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
			  int k, int a_size, int normalize, double *subst_mtx, char *alphabet)
{
  /* k is a state index, p is a sequence position index */
  
  int a_index;
  double prf_column_length, subst_mtx_row_length;
  int query_index;
  
  query_index = get_alphabet_index_msa_query((msa_seq + (p * (a_size+1)))->query_letter, alphabet, a_size);
  if(normalize == NO) {
    for(a_index = 0; a_index < a_size; a_index++) {
      *(E + get_mtx_index(k, a_index, a_size)) += Eka_base *
	(double)((msa_seq + get_mtx_index(p, a_index, a_size+1))->share) *
	*(subst_mtx + get_mtx_index(query_index, a_index, a_size));
    }
  }
  else {
    prf_column_length = 0.0;
    for(a_index = 0; a_index < a_size; a_index++) {
      prf_column_length += pow(((msa_seq + get_mtx_index(p, a_index, a_size+1))->share),2);