source: tags/initial/ALIV3/BI_helix.hxx

#define HELIX_MAX_NON_ST 10

#define HELIX_AWAR_PAIR_TEMPLATE "Helix/pairs/%s"
#define HELIX_AWAR_SYMBOL_TEMPLATE "Helix/symbols/%s"

typedef enum {
        HELIX_NONE,
        HELIX_STRONG_PAIR,
        HELIX_PAIR,
        HELIX_WEAK_PAIR,
        HELIX_NO_PAIR,
        HELIX_USER0,
        HELIX_USER1,
        HELIX_USER2,
        HELIX_USER3,
        HELIX_DEFAULT,
        HELIX_NON_STANDART0,
        HELIX_NON_STANDART1,
        HELIX_NON_STANDART2,
        HELIX_NON_STANDART3,
        HELIX_NON_STANDART4,
        HELIX_NON_STANDART5,
        HELIX_NON_STANDART6,
        HELIX_NON_STANDART7,
        HELIX_NON_STANDART8,
        HELIX_NON_STANDART9,
        HELIX_NO_MATCH,
        HELIX_MAX
} BI_PAIR_TYPE;


class BI_helix {
        private:
        int _check_pair(char left, char right, BI_PAIR_TYPE pair_type);
        public:
                // read only section
        struct BI_helix_entry {
                long pair_pos;
                BI_PAIR_TYPE pair_type;
                char    *helix_nr;
        } *entries;
        // **read only:
        char    *pairs[HELIX_MAX];
        char    *char_bind[HELIX_MAX];
        long size;
        static char error[256];

        // ***** read and write
#ifdef _USE_AW_WINDOW
        BI_helix(AW_root *aw_root); 
#else
        BI_helix(void);
#endif
        ~BI_helix(void);        

        char *init(GBDATA *gb_main);
        char *init(GBDATA *gb_main, char *alignment_name,
                char *helix_nr_name, char *helix_name);
        char *init(GBDATA *gb_helix_nr,GBDATA *gb_helix,long size);
        char *init(char *helix_nr, char *helix, long size);

        int check_pair(char left, char right, BI_PAIR_TYPE pair_type);
                // returns 1 if bases form a pair

#ifdef _USE_AW_WINDOW
        char get_symbol(char left, char right, BI_PAIR_TYPE pair_type);

        int show_helix( void *device, int gc1 , char *sequence,
                AW_pos x, AW_pos y,
                AW_bitset filter,
                AW_CL cd1, AW_CL cd2);
#endif
};

#ifdef _USE_AW_WINDOW
AW_window *create_helix_props_window(AW_root *awr, AW_cb_struct * /*owner*/awcbs);
#endif