debug_funcs.c

马尔科夫模型的java版本实现

#include <stdlib.h>
#include <stdio.h>



#include "structs.h"


void dump_align_matrix(int nr_rows, int nr_cols, struct align_mtx_element_s *mtx)
{
  int i,j;
  struct align_mtx_element_s *mtx_tmp;
  mtx_tmp = mtx;
  
  printf("alignment matrix dump:\n");
  printf("nr rows: %d\n", nr_rows);
  printf("nr columns: %d\n", nr_cols);
  printf("scores:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%d  ", mtx_tmp->score);
      mtx_tmp++;
    }
    printf("\n");
  }
  printf("\n\n");

  mtx_tmp = mtx;

  printf("lasts:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%c  ", mtx->last);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_trans_matrix(int nr_rows, int nr_cols, double *mtx)
{
  int i,j;
  printf("transition 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("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_int_trans_matrix(int nr_rows, int nr_cols, int *mtx)
{
  int i,j;
  printf("transition 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_emiss_matrix(int nr_rows, int nr_cols, double *mtx)
{
  int i,j;
  printf("emission matrix dump:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_post_prob_matrix(int nr_rows, int nr_cols, double *mtx)
{
  int i,j;
  printf("posterior probability matrix dump:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_forward_matrix(int nr_rows, int nr_cols, struct forward_s *mtx)
{
  int i,j;
  printf("forward matrix dump:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", mtx->prob);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_viterbi_matrix(int nr_rows, int nr_cols, struct viterbi_s *mtx)
{
  int i,j;
  struct viterbi_s *mtx_2;
  
  mtx_2 = mtx;
  printf("viterbi matrix dump probs:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      //printf("%d  ", mtx->prev);
       printf("%f  ", mtx->prob);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");

  printf("viterbi matrix dump prevs:\n");
  for(i = 0; i < nr_rows; i++) {
    printf("row: %d\n", i);
    for(j = 0; j < nr_cols; j++) {
      printf("col: %d = %d  \n", j, mtx_2->prev);
      //printf("%f  ", mtx->prob);
      mtx_2++;
    }
    printf("nr_cols = %d\n", j);
    printf("\n");
  }
  printf("\n");
}

void dump_one_best_matrix(int nr_rows, int nr_cols, struct one_best_s *mtx)
{
  int i,j;
  printf("one best matrix dump:\n");
  printf("%4d  ", 0);
  for(j = 0; j < nr_cols; j++) {
      printf("%8d  ", j);
  }
  printf("\n");
  for(i = 0; i < nr_rows; i++) {
    printf("%4d  ", i);
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", mtx->prob);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_backward_matrix(int nr_rows, int nr_cols, struct backward_s *mtx)
{
  int i,j;
  printf("backward matrix dump:\n");
  for(i = 0; i < nr_rows; i++) {
    for(j = 0; j < nr_cols; j++) {
      printf("%f  ", mtx->prob);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_scaling_array(int len, double *mtx)
{
  int i;
  printf("scaling array dump\n");
  for(i = 0; i < len; i++) {
    printf("%d: %f ", i, *mtx);
    mtx++;
  }
  printf("\n");
}

void dump_from_trans_array(int nr_v, struct path_element **array)
{
  int i;
  struct path_element *cur;
  

  printf("\nfrom_trans_array_dump:\n");
  printf("nr_v = %d\n", nr_v);
  
  
  for(i = 0; i < nr_v; i++) {
    if((*(array + i))->vertex == END) {
      printf("no transitions to vertex %d\n", i);
    }
    else {
      printf("paths to vertex %d:\n", i);
      cur = *(array + i);
      while(cur->vertex != END) {
	printf("%d ", cur->vertex);
	while(cur->next != NULL) {
	  cur = cur->next;
	  printf("%d ", cur->vertex);
	}
	printf("%d ", i);
	printf("\n");
	cur++;
      }
    }
  }
  printf("\n");
}

void dump_subst_mtx(double *mtx, int a_size)
{
  int i,j;
  int nr_rows = a_size + 1;
  int nr_cols = a_size;
  printf("substitution 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("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_to_trans_array(int nr_v, struct path_element **array)
{
  int i;
  struct path_element *cur;
  

  printf("\nto_trans_array_dump:\n");
  printf("nr_v = %d\n", nr_v);
  
  for(i = 0; i < nr_v; i++) {
    if((*(array + i))->vertex == END) {
      printf("no transitions from vertex %d\n", i);
    }
    else {
      printf("paths from vertex %d:\n", i);
      cur = *(array + i);
      while(cur->vertex != END) {
	printf("%d ", i);
	printf("%d ", cur->vertex);
	while(cur->next != NULL) {
	  cur = cur->next;
	  printf("%d ", cur->vertex);
	}
	printf("\n");
	cur++;
      }
    }
  }
  printf("\n");
}


void dump_T_matrix(int nr_rows, int nr_cols, double *mtx)
{
  int i,j;
  printf("T 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("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

void dump_E_matrix(int nr_rows, int nr_cols, double *mtx)
{
  int i,j;
  printf("E 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("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
}

/* dumps most probable state path for given string (misses end state) */
void dump_viterbi_path(struct viterbi_s *cur, struct hmm_s *hmmp,
		       struct viterbi_s *viterbi_mtxp, int row, int row_size)
{
  struct path_element *p_el;

  if(cur->prev == 0) {
    p_el = cur->prevp;
    printf("0 ");
    while(p_el->next != NULL) {
      printf("%d ", p_el->vertex);
      p_el++;
    }
  }
  else {
    dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp,
		      viterbi_mtxp, row-1, row_size);
    p_el = cur->prevp;
    printf("%d ", cur->prev);
    while(p_el->next != NULL) {
      p_el++;
      printf("%d ", p_el->vertex);
    }
  }
}

void dump_viterbi_label_path(struct viterbi_s *cur, struct hmm_s *hmmp,
			     struct viterbi_s *viterbi_mtxp, int row, int row_size)
{
  struct path_element *p_el;

  if(cur->prev == 0) {
    p_el = cur->prevp;
    printf("0 ");
    while(p_el->next != NULL) {
      printf("%c ", *(hmmp->vertex_labels + p_el->vertex));
      p_el++;
    }
  }
  else {
    dump_viterbi_label_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp,
		      viterbi_mtxp, row-1, row_size);
    p_el = cur->prevp;
    printf("%c ", *(hmmp->vertex_labels + (int)(cur->prev)));
    //printf("%d ", (int)(cur->prev));
    while(p_el->next != NULL) {
      p_el++;
      printf("%c ", *(hmmp->vertex_labels + p_el->vertex));
    }
  }
}

void dump_modules(struct hmm_s *hmmp)
{
  int i,j;

  printf("\nModule dump:\n");
  for(i = 0 ; i < hmmp->nr_m; i++) {
    printf("module: %s", (*(hmmp->modules + i))->name);
    printf("nr_v: %d\n", (*(hmmp->modules + i))->nr_v);
    printf("vertices: ");
    for(j = 0; j < (*(hmmp->modules + i))->nr_v;j++) {
      printf("%d ",*(((*(hmmp->modules + i))->vertices) + j));
    }
    printf("\n");
  }

  
}

void dump_multi_modules(struct hmm_multi_s *hmmp)
{
  int i,j;

  printf("\nModule dump:\n");
  for(i = 0 ; i < hmmp->nr_m; i++) {
    printf("module: %s", (*(hmmp->modules + i))->name);
    printf("nr_v: %d\n", (*(hmmp->modules + i))->nr_v);
    printf("vertices: ");
    for(j = 0; j < (*(hmmp->modules + i))->nr_v;j++) {
      printf("%d ",*(((*(hmmp->modules + i))->vertices) + j));
    }
    printf("\n");
  }  
}

void dump_distrib_groups(int *distrib_groups, int nr_d)
{
  int i,j;

  printf("\ndistribution groups dump:\n");
  for(i = 0 ; i < nr_d; i++) {
    printf("Group %d: ", i+1);
    while(1) {
      if(*distrib_groups == END) {
	distrib_groups++;
	printf("\n");
	break;
      }
      else {
	printf("%d ", *distrib_groups);
	distrib_groups++;
      }
    }
    printf("\n");
  }
  printf("\n");
}

void dump_trans_tie_groups(struct transition_s *trans_tie_groups, int nr_ttg)
{
  int i,j;

  printf("\ntrans tie groups dump:\n");
  for(i = 0 ; i < nr_ttg; i++) {
    printf("Tie %d: ", i+1);
    while(1) {
      if(trans_tie_groups->from_v == END) {
	trans_tie_groups++;
	printf("\n");
	break;
      }
      else {
	printf("%d->%d ", trans_tie_groups->from_v, trans_tie_groups->to_v);
	trans_tie_groups++;
      }
    }
    printf("\n");
  }
  printf("\n");
}

void dump_prior_struct(struct emission_dirichlet_s *emission_priorsp)
{
  int i,j;
  double *mtx = emission_priorsp->prior_values;
  
  printf("prifile: %s\n", emission_priorsp->name);
  printf("nr components: %d\n", emission_priorsp->nr_components);
  printf("q_values: ");
  for(i = 0; i < emission_priorsp->nr_components; i++) {
    printf("%f ", *((emission_priorsp->q_values) + i));
  }
  printf("\n");
  printf("alpha_sums: ");
  for(i = 0; i < emission_priorsp->nr_components; i++) {
    printf("%f ", *((emission_priorsp->alpha_sums) + i));
  }
  printf("\n");
  printf("alpha_values:\n");
  for(i = 0; i < emission_priorsp->nr_components; i++) {
    for(j = 0; j < emission_priorsp->alphabet_size; j++) {
      printf("%f  ", *mtx);
      mtx++;
    }
    printf("\n");
  }
  printf("\n");
  
  printf("logbeta_values: ");
  for(i = 0; i < emission_priorsp->nr_components; i++) {
    printf("%f ", *((emission_priorsp->logbeta_values) + i));
  }
  printf("\n");
}

void dump_silent_vertices(struct hmm_s *hmmp)
{
  int i;

  printf("silent vertices dump: ");
  for(i = 0;;i++) {
    if(*(hmmp->silent_vertices + i) == END) {
      break;
    }
    else {
      printf("%d ", *(hmmp->silent_vertices + i));
    }
  }
  printf("\n");
}

void dump_silent_vertices_multi(struct hmm_multi_s *hmmp)
{
  int i;

  printf("silent vertices dump: ");
  for(i = 0;;i++) {
    if(*(hmmp->silent_vertices + i) == END) {
      break;
    }
    else {
      printf("%d ", *(hmmp->silent_vertices + i));
    }
  }
  printf("\n");
}

void dump_locked_vertices(struct hmm_s *hmmp)
{
  int i;

  printf("locked vertices dump: ");
  for(i = 0;;i++) {
    if(*(hmmp->locked_vertices + i) == END) {
      break;
    }
    else {
      printf("%d ", *(hmmp->locked_vertices + i));
    }
  }
  printf("\n");
}


void dump_seq(struct letter_s *seq)
{
  int i;
  
  while(seq->letter[0] != '\0') {
    i = 0;
    while(seq->letter[i] != '\0') {
      printf("%c", seq->letter[i]);
      i++;
    }
    printf(";");
    seq++;
  }
  printf("\n");
}

void dump_seqs(struct sequences_s *seq_infop)