debug_funcs.c

马尔科夫模型的java版本实现

{
  int i,j;
  struct letter_s *seqsp;


  printf("seqs dump\n");
  for(i = 0; i < seq_infop->nr_seqs; i++) {
    seqsp = (seq_infop->seqs + i)->seq;
    printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
    printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
    while(seqsp->letter[0] != '\0') {
      j = 0;
      while(seqsp->letter[j] != '\0') {
	printf("%c", seqsp->letter[j]);
	j++;
      }
      printf(";");
      seqsp++;
    }
    printf("\n");
  }
}

void dump_seqs_multi(struct sequences_multi_s *seq_infop)
{
  int i,j,k;
  struct letter_s *seqsp;
  
  printf("multi alphabet seqs dump\n");
  printf("nr_seqs = %d\n", seq_infop->nr_seqs);
  printf("longest_seq = %d\n", seq_infop->longest_seq);
  printf("shortest_seq = %d\n", seq_infop->shortest_seq);
  printf("avg_seq_len = %d\n", seq_infop->avg_seq_len);
  for(i = 0; i < seq_infop->nr_seqs; i++) {
    for(k = 0; k < seq_infop->nr_alphabets; k++) {
      if(k == 0) {
	seqsp = (seq_infop->seqs + i)->seq_1;
      }
      if(k == 1) {
	seqsp = (seq_infop->seqs + i)->seq_2;
      }
      if(k == 2) {
	seqsp = (seq_infop->seqs + i)->seq_3;
      }
      if(k == 3) {
	seqsp = (seq_infop->seqs + i)->seq_4;
      }
      printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
      printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
      while(seqsp->letter[0] != '\0') {
	j = 0;
	while(seqsp->letter[j] != '\0') {
	  printf("%c", seqsp->letter[j]);
	  j++;
	}
	printf(";");
	seqsp++;
      }
      printf("\n");
    }
  }
}

void dump_labeled_seqs_multi(struct sequences_multi_s *seq_infop)
{
  int i,j,k;
  struct letter_s *seqsp;

  printf("seqs dump\n");
  for(i = 0; i < seq_infop->nr_seqs; i++) {
    for(k = 0; k < seq_infop->nr_alphabets; k++) {
      if(k == 0) {
	seqsp = (seq_infop->seqs + i)->seq_1;
      }
      if(k == 1) {
	seqsp = (seq_infop->seqs + i)->seq_2;
      }
      if(k == 2) {
	seqsp = (seq_infop->seqs + i)->seq_3;
      }
      if(k == 3) {
	seqsp = (seq_infop->seqs + i)->seq_4;
      }
      printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
      printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
      while(seqsp->letter[0] != '\0') {
	j = 0;
	while(seqsp->letter[j] != '\0') {
	  printf("%c", seqsp->letter[j]);
	  j++;
	}
	if(k == 0) {
	  printf("/%c",seqsp->label);
	}
	printf(";");
	seqsp++;
      }
      printf("\n");
    }
  }
}

void dump_labeled_seqs(struct sequences_s *seq_infop)
{
  int i,j;
  struct letter_s *seqsp;

  printf("seqs dump\n");
  for(i = 0; i < seq_infop->nr_seqs; i++) {
    seqsp = (seq_infop->seqs + i)->seq;
    printf("seq_name = %s\n", (seq_infop->seqs + i)->name);
    printf("seq_length = %d\n", (seq_infop->seqs + i)->length);
    while(seqsp->letter[0] != '\0') {
      j = 0;
      while(seqsp->letter[j] != '\0') {
	printf("%c", seqsp->letter[j]);
	j++;
      }
      printf("/%c",seqsp->label);
      printf(";");
      seqsp++;
    }
    printf("\n");
  }
}


void dump_msa_seqs(struct msa_sequences_s *msa_seq_infop, int a_size)
{
  int i,j;
  int *cur_pos;

  cur_pos = (int*)(msa_seq_infop->gaps + msa_seq_infop->msa_seq_length);
  printf("msa seqs dump:\n");
  printf("nr_seqs = %d\n", msa_seq_infop->nr_seqs);
  printf("msa_seq_length = %d\n", msa_seq_infop->msa_seq_length);
  printf("nr_lead_columns = %d\n", msa_seq_infop->nr_lead_columns);
  for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
    printf("pos %d: ", i+1);
    printf("\n");
    printf("label: %c\n", (msa_seq_infop->msa_seq + get_mtx_index(i,0,a_size+1))->label);
    for(j = 0; j < a_size+1; j++) {
      printf("%f ",(msa_seq_infop->msa_seq + get_mtx_index(i,j,a_size+1))->nr_occurences); 
    }
    printf("\n");
    for(j = 0; j < a_size+1; j++) {
      printf("%f ",(msa_seq_infop->msa_seq + get_mtx_index(i,j,a_size+1))->share); 
    }
    printf("\n");
    for(j = 0; j < a_size+1; j++) {
      printf("%f ",(msa_seq_infop->msa_seq + get_mtx_index(i,j,a_size+1))->prior_share); 
    }
    printf("\n");
  }
  printf("\n");
  printf("gaps:\n");
  for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
    printf("pos %d: ",i+1);
    while(*cur_pos != END) {
      printf("%d ", *cur_pos);
      cur_pos++;
    }
    printf("\n");
    cur_pos++;
  }

  printf("lead columns: ");
  i = 0;
  while(*(msa_seq_infop->lead_columns_start + i) != END) {
    printf("%d ", *(msa_seq_infop->lead_columns_start + i));
    i++;
  }
  printf("\n");

  printf("gap_shares: ");
  for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
    printf("%f ", *(msa_seq_infop->gap_shares + i));
  }
  printf("\n\n");
}

void dump_msa_seqs_multi(struct msa_sequences_multi_s *msa_seq_infop, struct hmm_multi_s *hmmp)
{
  int i,j;
  int *cur_pos;

  cur_pos = (int*)(msa_seq_infop->gaps + msa_seq_infop->msa_seq_length);
  printf("msa seqs dump:\n");

  printf("nr_seqs = %d\n", msa_seq_infop->nr_seqs);
  printf("msa_seq_length = %d\n", msa_seq_infop->msa_seq_length);
  printf("nr_lead_columns = %d\n\n", msa_seq_infop->nr_lead_columns);
  
  printf("Alphabet 1\n");
  for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
    printf("pos %d: ", i+1);
    printf("\n");
    printf("label: %c\n", (msa_seq_infop->msa_seq_1 + get_mtx_index(i,0,hmmp->a_size+1))->label);
    for(j = 0; j < hmmp->a_size+1; j++) {
      printf("%f ",(msa_seq_infop->msa_seq_1 + get_mtx_index(i,j,hmmp->a_size+1))->nr_occurences); 
    }
    printf("\n");
    for(j = 0; j < hmmp->a_size+1; j++) {
      printf("%f ",(msa_seq_infop->msa_seq_1 + get_mtx_index(i,j,hmmp->a_size+1))->share); 
    }
    printf("\n");
    for(j = 0; j < hmmp->a_size+1; j++) {
      printf("%f ",(msa_seq_infop->msa_seq_1 + get_mtx_index(i,j,hmmp->a_size+1))->prior_share); 
    }
    printf("\n");
  }
  printf("\n");
  
  if(hmmp->nr_alphabets > 1) {
    printf("Alphabet 2\n");
    for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
      printf("pos %d: ", i+1);
      printf("\n");
      printf("label: %c\n", (msa_seq_infop->msa_seq_2 + get_mtx_index(i,0,hmmp->a_size_2+1))->label);
      for(j = 0; j < hmmp->a_size_2+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_2 + get_mtx_index(i,j,hmmp->a_size_2+1))->nr_occurences); 
      }
      printf("\n");
      for(j = 0; j < hmmp->a_size_2+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_2 + get_mtx_index(i,j,hmmp->a_size_2+1))->share); 
      }
      printf("\n");
      for(j = 0; j < hmmp->a_size_2+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_2 + get_mtx_index(i,j,hmmp->a_size_2+1))->prior_share); 
      }
      printf("\n");
    }
    printf("\n");
  }

  if(hmmp->nr_alphabets > 2) {
    printf("Alphabet 3\n");
    for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
      printf("pos %d: ", i+1);
      printf("\n");
      printf("label: %c\n", (msa_seq_infop->msa_seq_3 + get_mtx_index(i,0,hmmp->a_size_3+1))->label);
      for(j = 0; j < hmmp->a_size_3+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_3 + get_mtx_index(i,j,hmmp->a_size_3+1))->nr_occurences); 
      }
      printf("\n");
      for(j = 0; j < hmmp->a_size_3+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_3 + get_mtx_index(i,j,hmmp->a_size_3+1))->share); 
      }
      printf("\n");
      for(j = 0; j < hmmp->a_size_3+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_3 + get_mtx_index(i,j,hmmp->a_size_3+1))->prior_share); 
      }
      printf("\n");
    }
    printf("\n");
  }

  if(hmmp->nr_alphabets > 3) {
    printf("Alphabet 4\n");
    for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
      printf("pos %d: ", i+1);
      printf("\n");
      printf("label: %c\n", (msa_seq_infop->msa_seq_4 + get_mtx_index(i,0,hmmp->a_size_4+1))->label);
      for(j = 0; j < hmmp->a_size_4+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_4 + get_mtx_index(i,j,hmmp->a_size_4+1))->nr_occurences); 
      }
      printf("\n");
      for(j = 0; j < hmmp->a_size_4+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_4 + get_mtx_index(i,j,hmmp->a_size_4+1))->share); 
      }
      printf("\n");
      for(j = 0; j < hmmp->a_size_4+1; j++) {
	printf("%f ",(msa_seq_infop->msa_seq_4 + get_mtx_index(i,j,hmmp->a_size_4+1))->prior_share); 
      }
      printf("\n");
    }
    printf("\n");
  }

  
  printf("gaps:\n");
  
  for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
    printf("pos %d: ",i+1);
    while(*cur_pos != END) {
      printf("%d ", *cur_pos);
      cur_pos++;
    }
    printf("\n");
    cur_pos++;
  }

  
  printf("lead columns: ");
  i = 0;
  while(*(msa_seq_infop->lead_columns_start + i) != END) {
    printf("%d ", *(msa_seq_infop->lead_columns_start + i));
    i++;
  }
  printf("\n");

  printf("gap_shares: ");
  for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
    printf("%f ", *(msa_seq_infop->gap_shares + i));
  }
  printf("\n\n");
}


void dump_replacement_letters(struct replacement_letter_s *replacement_letters, int a_size)
{
  int i,j;
  int nr_rows, nr_cols;
  double *prob_mtx;

  prob_mtx = replacement_letters->probs;
  nr_rows = replacement_letters->nr_rl;
  nr_cols = a_size;
  
  
  printf("replacement letter dump:\n");
  printf("nr_letters = %d\n", replacement_letters->nr_rl);
  printf("letters: ");
  for(i = 0; i < nr_rows;i++) {
    printf("%c ", (*(replacement_letters->letters + i)));
  }
  printf("\nprobs:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", *prob_mtx);
      prob_mtx++;;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_replacement_letters_multi(struct replacement_letter_multi_s *replacement_letters, int alphabet, int a_size)
{
  int i,j;
  int nr_rows, nr_cols;
  double *prob_mtx;

  if(alphabet == 1) {
    prob_mtx = replacement_letters->probs_1;
    nr_rows = replacement_letters->nr_rl_1;
  }
  if(alphabet == 2) {
    prob_mtx = replacement_letters->probs_2;
    nr_rows = replacement_letters->nr_rl_2;
  }
  if(alphabet == 3) {
    prob_mtx = replacement_letters->probs_3;
    nr_rows = replacement_letters->nr_rl_3;
  }
  if(alphabet == 4) {
    prob_mtx = replacement_letters->probs_4;
    nr_rows = replacement_letters->nr_rl_4;
  }
  nr_cols = a_size;
  
  
  printf("replacement letter dump:\n");
  if(alphabet == 1) {
    printf("nr_letters = %d\n", replacement_letters->nr_rl_1);
  }
  if(alphabet == 2) {
    printf("nr_letters = %d\n", replacement_letters->nr_rl_2);
  }
  if(alphabet == 3) {
    printf("nr_letters = %d\n", replacement_letters->nr_rl_3);
  }
  if(alphabet == 4) {
    printf("nr_letters = %d\n", replacement_letters->nr_rl_4);
  }
  printf("letters: ");
  for(i = 0; i < nr_rows;i++) {
    if(alphabet == 1) {
      printf("%c ", (*(replacement_letters->letters_1 + i)));
    }
    if(alphabet == 2) {
      printf("%c ", (*(replacement_letters->letters_2 + i)));
    }
    if(alphabet == 3) {
      printf("%c ", (*(replacement_letters->letters_3 + i)));
    }
    if(alphabet == 4) {
      printf("%c ", (*(replacement_letters->letters_4 + i)));
    }
  }
  printf("\nprobs:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", *prob_mtx);
      prob_mtx++;;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_calibration_matrix(int nr_rows, int nr_cols, int *mtx)
{
  int i,j;
  printf("calibration matrix dump:\n");
  printf("nr rows: %d\n", nr_rows);
  printf("nr columns: %d\n", nr_cols);
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%d  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_to_silent_trans_array(int nr_v, int **array)
{
  int i;
  int pos;

  printf("To_silent_trans_array_dump:\n");
  for(i = 0; i < nr_v; i++) {
    printf("Transitions from vertex %d: ", i);
    pos = 0;
    while(*(*(array + i) + pos) != END) {
      printf("%d ", *(*(array + i) + pos));
      pos++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_aa_distrib_mtx(struct aa_distrib_mtx_s *aa_distrib_mtxp)
{
  int i;

  printf("aa_distrib_mtx_dump\n");
  printf("a_size = %d\n", aa_distrib_mtxp->a_size);
  for(i = 0; i < aa_distrib_mtxp->a_size;i++) {
    printf("%f %f %f\n", *(aa_distrib_mtxp->inside_values + i), *(aa_distrib_mtxp->outside_values + i),
	   *(aa_distrib_mtxp->membrane_values + i));
  }
}


void dump_v_list(int *sorted_v_list)
{
  int i = 0;
  printf("v-list dump:\n");
  while(*(sorted_v_list + i) != -99) {
    if(*(sorted_v_list + i) == -9) {
      printf(" | ");
    }
    else {
      printf("%d ", *(sorted_v_list + i));
    }
    i++;
  }
  printf("\n");
}

void dump_labeling(char *labeling, int c)
{
  int i;
  
  printf("labeling dump:\n");
  if(labeling == NULL) {
    printf("NULL\n");
    return;
  }
  for(i = 1; i <= c; i++) {
    printf("%c",labeling[i]);
  }
  printf("\n");
}

void dump_label_tmp_list(int *list)
{
  int i;

  printf("label_list_dump: \n");
  
  for(i = 0; list[i] != TOT_END;i++) {
    printf("%d ",list[i]);
  }
  printf("\n");
}

void dump_labels(char *labels, int nr_labels)
{
  int i;

  printf("label_dump: \n");
  for(i = 0; i < nr_labels; i++) {
    printf("%c ", labels[i]);
  }
  printf("\n");
}

void check_for_corrupt_values(int nr_rows, int nr_cols, double *mtx, char *name)
{
  int v,w;
  int x;

  /* test if this matrix contains strange values */
  for(v = 0; v < nr_rows; v++) {
    for(w = 0; w < nr_cols; w++) {
      x = get_mtx_index(v,w,nr_cols);
      if(*(mtx + x) < 0.0) {
	printf("%s[%d][%d] = %f\n", name, v,w,*(mtx + x));
	if(*(mtx + x) == 0.0) {
	}
      }
      else if(!(*(mtx + x) <= 1000000000000.0)) {
	printf("%s[%d][%d] = %f\n", name, v,w,*(mtx + x));
      }
      else {
	//printf("%s[%d][%d] = %f\n", name, v,w,*(mtx + x));
      }
    }
  } 
}

void dump_weights(double *weights, int nr_seqs)
{
  int i;

  printf("weight dump:\n");
  for(i = 0; i < nr_seqs; i++) {
    printf("%f\n", *(weights + i));
  }
}