structs.h

马尔科夫模型的java版本实现

  int a_size_3;
  int a_size_4;
  char alphabet[1000];
  char alphabet_2[1000];
  char alphabet_3[1000];
  char alphabet_4[1000];
  double *emissions;
  double *emissions_2;
  double *emissions_3;
  double *emissions_4;
  
};


/* Structure: module_s
 *
 * Declaration of module
 */
struct module_s {
  char name[50];
  int type;
  int v_type;
  int nr_v;
  int *vertices;
  char priorfile_name[200];
};


/* Structure: module_multi_s
 *
 * Declaration of module
 */
struct module_multi_s {
  char name[50];
  int type;
  int v_type;
  int nr_v;
  int *vertices;
  char priorfile_name[200];
  char priorfile_name_2[200];
  char priorfile_name_3[200];
  char priorfile_name_4[200];
};

/* Structure emission_dirichlet_s
 *
 * Declaration of dirichlet mixture 
 */
struct emission_dirichlet_s {
  char name[200];
  int nr_components;
  int alphabet_size;
  double *q_values; /* each component's "probability" */
  double *alpha_sums; /* sums of the prior values */
  double *logbeta_values; /* precalculated beta values B(alpha) for each alpha */
  double *prior_values; /* matrix with prior values */
};


/* Structure: viterbi_s
 *
 * Declaration of viterbi matrix element
 */

struct viterbi_s {
  double prob; /* is really a log prob */
  int prev;
  struct path_element *prevp;
};

/* Structure: forward_s
 *
 * Declaration of forward matrix element
 */

struct forward_s {
  double prob;
  //int distance_to_next;
};

/* Structure: backward_s
 *
 * Declaration of backward matrix element
 */

struct backward_s {
  double prob;
  //int distance_to_next;
};

/* Structure: one_best_s
 *
 * Declaration of one_best matrix element
 */

struct one_best_s {
  double prob;
  int is_updated;
  char *labeling;
};



/* Structure: letter_prob_s
 *
 * Declaration of letter probability distribution element
 */
struct letter_prob_s {
  char letter;
  double share;
};


/* Structure: path_element
 *
 * Declaration of trans_array elements
 */
struct path_element {
  int vertex;
  struct path_element *next;
};

/* Structure: letter_s
 *
 * Declaration of alphabet symbol
 */
struct letter_s {
  char letter[5];
  char label;
  double cont_letter;
};

/* Structure: sequence_s
 *
 * Declaration of sequence info holder
 */
struct sequence_s {
  char name[MAX_SEQ_NAME_SIZE];
  int length;
  double weight;
  struct letter_s *seq;
};

/* Structure: sequence_multi_s
 *
 * Declaration of sequence info holder for multiple alphabet sequences
 */
struct sequence_multi_s {
  char name[MAX_SEQ_NAME_SIZE];
  int length;
  double weight;
  struct letter_s *seq_1;
  struct letter_s *seq_2;
  struct letter_s *seq_3;
  struct letter_s *seq_4;
};


/* Structure: sequences_s
 *
 * Declaration of struct for info about the sequences
 */

struct sequences_s {
  int nr_seqs;
  int longest_seq;
  int shortest_seq;
  int avg_seq_len;
  struct sequence_s *seqs;
};


/* Structure: sequences_multi_s
 *
 * Declaration of struct for info about the sequences
 */
struct sequences_multi_s {
  int nr_alphabets;
  int nr_seqs;
  int longest_seq;
  int shortest_seq;
  int avg_seq_len;
  struct sequence_multi_s *seqs;
};


/* Structure: MSA_letter_s
 *
 * Declaration of struct for MSA_letter
 */
struct msa_letter_s {
  double nr_occurences; /* non integer occurences exist */
  double share;
  double prior_share;
  char label;
  char query_letter[5];
  double cont_letter;
};

/* Structure: msa_sequences_s
 *
 * Declaration of struct for msa sequence info
 */
struct msa_sequences_s {
  int nr_seqs;
  int msa_seq_length;
  int nr_lead_columns;
  struct msa_letter_s *msa_seq;
  int **gaps;
  int *lead_columns_start;
  int *lead_columns_end;
  double *gap_shares;
};

/* Structure: msa_sequences_multi_s
 *
 * Declaration of struct for msa sequence info
 */
struct msa_sequences_multi_s {
  int nr_alphabets;
  int nr_seqs;
  int msa_seq_length;
  int nr_lead_columns;
  struct msa_letter_s *msa_seq_1;
  struct msa_letter_s *msa_seq_2;
  struct msa_letter_s *msa_seq_3;
  struct msa_letter_s *msa_seq_4;
  int **gaps;
  int *lead_columns_start;
  int *lead_columns_end;
  double *gap_shares;
};


/* Structure: replacement_letter_s
 *
 * Declaration of struct for replacement letter info
 */
struct replacement_letter_s {
  int nr_rl;
  struct letter_s *letters;
  double *probs;
};

/* Structure: replacement_letter_multi_s
 *
 * Declaration of struct for replacement letter info
 */
struct replacement_letter_multi_s {
   int nr_alphabets;
   int nr_rl_1;
   int nr_rl_2;
   int nr_rl_3;
   int nr_rl_4;
   struct letter_s *letters_1;
   double *probs_1;
   struct letter_s *letters_2;
   double *probs_2;
   struct letter_s *letters_3;
   double *probs_3;
   struct letter_s *letters_4;
   double *probs_4;
 };

/* Structure: aa_distrib_mtx_s
 *
 * Declaration of struct for amino acid distribution matrix
 */
struct aa_distrib_mtx_s {
  int a_size;
  double *inside_values;
  double *outside_values;
  double *membrane_values;
};


/* Structure: v_list_element_s
 *
 * Declaration of struct for n_best v_list elements
 */
struct v_list_element_s {
  int vertex; /* vertex nr */
  int address; /* pointer address of this vertex's labeling */
};

/* Structure: transition_s
 *
 * Declaration of struct for transition (used for transition ties)
 */
struct transition_s {
  int from_v;
  int to_v;
};

struct align_mtx_element_s {
  int score;
  char last;
};

struct alignment_s {
  int target_pos;
  int template_pos;
  char target_letter[5];
  char template_letter[5];
};