ARB
AP_pos_var.h
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1 // =============================================================== //
2 // //
3 // File : AP_pos_var.h //
4 // Purpose : provides PVP calculation //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #ifndef AP_POS_VAR_H
12 #define AP_POS_VAR_H
13 
14 #ifndef ARBTOOLS_H
15 #include <arbtools.h>
16 #endif
17 #ifndef ARBDB_H
18 #include <arbdb.h>
19 #endif
20 
21 class AW_window;
22 class AW_root;
23 class arb_progress;
24 
25 class AP_pos_var : virtual Noncopyable {
26  GBDATA *gb_main;
27 
28  long treeLeafs; // number of leafs in tree
29  long treeNodes; // number of leafs + inner nodes in tree
30 
31  arb_progress *progress;
32 
33  GB_UINT4 *frequencies[256]; // count every occurrence
34  GB_UINT4 *transitions; // minimum transitions
35  GB_UINT4 *transversions; // minimum transversions (dna only)
36 
37  unsigned char char_2_freq[256]; // mapper (~ toupper)
38 
39  long char_2_transition[256]; // a->1 c->2 g->4 ...
40  long char_2_transversion[256]; // y->1 r->2
41 
42  long ali_len; // max len of alignment
43  char *ali_name;
44  char *tree_name;
45  bool is_nuc;
46 
47  const char *parsimony(TreeNode *tree, GB_UINT4 *bases = NULp, GB_UINT4 *ltbases = NULp);
48 
49 public:
50 
51  AP_pos_var(GBDATA *gb_main_, const char *ali_name_, long ali_len_, bool is_nuc_, const char *tree_name_);
52  ~AP_pos_var();
53 
54  GB_ERROR retrieve(TreeNode *tree);
55  GB_ERROR delete_aliEntry_from_SAI(const char *sai_name);
56  GB_ERROR save_aliEntry_to_SAI(const char *sai_name);
57 };
58 
59 #else
60 #error AP_pos_var.h included twice
61 #endif // AP_POS_VAR_H
unsigned int GB_UINT4
Definition: arbdb_base.h:37
GB_ERROR save_aliEntry_to_SAI(const char *sai_name)
Definition: AP_pos_var.cxx:215
GB_ERROR delete_aliEntry_from_SAI(const char *sai_name)
Definition: AP_pos_var.cxx:202
AP_pos_var(GBDATA *gb_main_, const char *ali_name_, long ali_len_, bool is_nuc_, const char *tree_name_)
Definition: AP_pos_var.cxx:23
GB_ERROR retrieve(TreeNode *tree)
Definition: AP_pos_var.cxx:125
#define NULp
Definition: cxxforward.h:97