source: branches/port5/NTREE/ap_pos_var_pars.hxx

Last change on this file was 5825, checked in by westram, 16 years ago
  • replaced GB_entry/GB_create/GB_search+GB_read_XXX by GBT_read_XXX
  • improved error handling in many functions
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.2 KB
Line 
1#define AWAR_PVP_SAI "tmp/pos_var_pars/sai"
2#define AWAR_PVP_TREE "tmp/pos_var_pars/tree"
3
4AW_window *AP_open_pos_var_pars_window( AW_root *root );
5
6class AP_pos_var {
7    GBDATA        *gb_main;
8    long           timer;       // for the status box
9    long           treesize;    // max value for slider
10    GB_UINT4      *frequencies[256]; // count every occurrence
11    GB_UINT4      *transitions; // minumum transitions
12    GB_UINT4      *transversions; // minimum transversions (dna only)
13    unsigned char  char_2_freq[256]; // mapper (~ toupper)
14    long           char_2_transition[256]; // a->1 c->2 g->4 ...
15    long           char_2_transversion[256]; // y->1 r->2
16
17    long  getsize(GBT_TREE *tree); // size of tree
18    long  ali_len;              // max len of alignment
19    long  is_dna;
20    char *ali_name;
21    char *tree_name;
22
23    const char *parsimony(GBT_TREE *tree, GB_UINT4 *bases = 0, GB_UINT4 *ltbases = 0);
24
25public:
26
27    AP_pos_var(GBDATA *gb_main,char *ali_name, long ali_len, int isdna, char *tree_name);
28    ~AP_pos_var();
29
30    GB_ERROR retrieve(GBT_TREE *tree);
31    GB_ERROR delete_old_sai(const char *sai_name);
32    GB_ERROR save_sai(const char *sai_name);
33};
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