source: tags/initial/CAT/cat_tree.hxx

#ifndef cat_tree_hxx_included
#define cat_tree_hxx_included

#ifndef GB_INCLUDED
struct GBDATA;
#endif

enum {                          // COLOR SCHEME (orable)
        T2J_COLOR_UNKNOWN = 0,
        T2J_COLOR_YES = 1,
        T2J_COLOR_NO = 2,
        T2J_COLOR_BOTH = 3
};


enum CAT_FIELDS {
        CAT_FIELD_NAME,         // internal id
        CAT_FIELD_FULL_NAME,    // fullname
        CAT_FIELD_GROUP_NAME,   // name of internal nodes
        CAT_FIELD_ACC,          // accession number
        CAT_FIELD_STRAIN,       // first strain word
        CAT_FIELD_MAX
};

#define CAT_INIT_STRING_FILE_SIZE 10000

typedef enum {
        CAT_TRUE = 1,
        CAT_FALSE = 0
}       CAT_BOOL;

typedef long CAT_node_id;

typedef enum {
        CAT_NUMBERING_LEAFS_ONLY,
        CAT_NUMBERING_LEVELS,
        CAT_NUMBERING_MAX
} CAT_NUMBERING;

class CAT_node {
        public:
        CAT_node_id             father;         // == 0 if root
        CAT_node_id             leftson;        // == 0 if leaf
        CAT_node_id             rightson;
        long            nleafs;                 // count all the leafs
        long            numbering[CAT_NUMBERING_MAX];   // all leafes are numbered from left to right
        long            deep;
        unsigned char   color_in;               // imported from ARB
        unsigned char   is_grouped_in;          // imported from ARB !!! 0 expanded  1 grouped
        unsigned char   color;  
        unsigned char   is_grouped;             // 0 expanded  1 grouped
        unsigned char   branch_length_byte;
        float           branch_length_float;
        long            field_offsets[CAT_FIELD_MAX];   // offset in 
                                // CAT_tree->data
        char            *user_data;
};

struct CAT_tree {

        public:
        /********* READ ONLY *************/
        char    data[4];                        // array of strings, holds
                                                // all the words
        int nnodes;
        CAT_node nodes[1];                      // array of nodes (note 1 is
                                                // replaced by nnodes !!!
                                                // data is organized as nlr
};

CAT_tree *new_CAT_tree(int size);


inline CAT_tree *load_CAT_tree(const char *path){
        return (CAT_tree *)GB_map_file(path,1);
}

typedef struct gbt_tree_struct  GBT_TREE;


const char *create_and_save_CAT_tree(GBDATA *gb_main, const char *tree_name, const char *path);
const char *create_and_save_CAT_tree(GBT_TREE *tree, const char *path);




#endif