source: tags/initial/NALIGNER/ali_preali.hxx

#include "ali_profile.hxx"

class ALI_PREALI {
private:
   long (*helix)[];
        char (*helix_border)[];
        unsigned long helix_len;

        ALI_PROFILE prof;

   char normalize_char(char in);
   long normalize_sequence(char *gen_seq, char **norm_seq);
        void print_table(char *norm_seq, char *path_matrix, long line, long col);
        int map_path(char *path_matrix, long pcol_len, long seq_map[],
                                         long col, long line);
        int prealigner(char *norm_seq, unsigned long norm_seq_len, long **seq_map);
   int get_sequence(char *norm_seq, unsigned long norm_seq_len, long *seq_map,
                                                  char **prealigned_seq, char **error_seq,
                                                  float cost_low, float cost_middle, float cost_high);
        int check_helix(char prealigned_seq[], char error_seq[], 
                                                 unsigned long seq_len, double (*bind_matrix) [5][5]);

   int find_next_helix(char h1[], long h_len, int start_pos,
                       int *helix_nr, int *start, int *end);
   int find_comp_helix(char h1[], long h_len, int start_pos,
                       int helix_nr, int *start, int *end);
   void delete_comp_helix(char h1[], char h2[], long h_len,
                       int start_pos, int end_pos);
   int map_helix(char h2[], long h_len, int start1, int end1,
                 int start2, int end2);
   int make_helix(char *h1, char *h2);
        int make_intervalls(char *prealigned_seq, char *error_seq,
                                                          unsigned long seq_len,
                                                          int intervall_border, int intervall_center,
                                                          char **intervall_seq);

public:
        int insert_reference(char *gen_seq, double weight = 1.0);
        int calculate_costs(double *cost_matrix);
        int prealign_sequence(char *gen_seq, char *helix1, char *helix2,
                              char **prealigned_seq, char **error_seq,
                                                                 char **intervall_seq,
                                                                 float cost_low, float cost_middle, float cost_high,
                                                                 double *bind_matrix,
                                                                 int intervall_border, int intervall_center);
        int get_reference(char **reference);
        int get_helix_border(char **border);
};