source: tags/initial/NTREE/ap_pos_var_pars.hxx

#define AWAR_PVP_SAI "tmp/pos_var_pars/sai"
#define AWAR_PVP_TREE "tmp/pos_var_pars/tree"

AW_window *AP_open_pos_var_pars_window( AW_root *root );

class AP_pos_var {
    GBDATA *gb_main;
    long        timer;                  // for the status box
    long        treesize;               // max value for slider
    GB_UINT4 *frequencies[256];         // count every occurrence
    GB_UINT4 *transitions;              // minumum transitions
    GB_UINT4 *transversions;            // minimum transversions (dna only)
    unsigned char char_2_freq[256];     // mapper (~ toupper)
    long char_2_transition[256];        // a->1 c->2 g->4 ...
    long char_2_transversion[256];      // y->1 r->2

    long        getsize(GBT_TREE *tree);        // size of tree
    long        ali_len;                        // max len of alignment
    long        is_dna;
    char        *ali_name;
    char        *tree_name;

    const char  *parsimony( GBT_TREE *tree, GB_UINT4 *bases =0, GB_UINT4 *ltbases =0 );

public:

    AP_pos_var(GBDATA *gb_main,char *ali_name, long ali_len, int isdna,
               char *tree_name);
    ~AP_pos_var();
    GB_ERROR retrieve( GBT_TREE *tree);
    char *delete_old_sai( char *sai_name );
    char *save_sai( char *sai_name );
};