ARB

#include "ap_tree_nlen.hxx"
#include "ap_main.hxx"
#include <AP_filter.hxx>
#include <arb_progress.h>
#include <cmath>
#include <iomanip>
Go to the source code of this file.
Classes  
class  MutationsPerSite 
Functions  
static void  buildSonEdges (AP_tree_nlen *node) 
static double  ap_calc_bootstrap_remark_sub (int seq_len, const char *old, const char *ne) 
static void  ap_calc_bootstrap_remark (AP_tree_nlen *son_node, AP_BL_MODE mode, const MutationsPerSite &mps) 
void  update_undefined_leaf_branchlength (AP_tree_nlen *leaf) 
bool  allBranchlengthsAreDefined (AP_tree_nlen *tree) 
void  undefine_branchlengths (AP_tree_nlen *node) 
ostream &  operator<< (ostream &out, const AP_tree_edge *e) 
Variables  
const GBT_LEN  AP_UNDEF_BL = 10.5 

static 
Builds edges between a node and his two sons. We assume there is already an edge to node's father and there are no edges to his sons.
Definition at line 39 of file AP_tree_edge.cxx.
Referenced by AP_tree_edge::initialize().

static 
Definition at line 272 of file AP_tree_edge.cxx.
References diff(), GB_log_fak(), and max.
Referenced by ap_calc_bootstrap_remark().

static 
Definition at line 344 of file AP_tree_edge.cxx.
References AP_BL_BOOTSTRAP_ESTIMATE, ap_calc_bootstrap_remark_sub(), and MutationsPerSite::data().
Referenced by AP_tree_edge::nni_rec().

inline 
Definition at line 365 of file AP_tree_edge.cxx.
References ap_assert, ap_main, AP_UNDEF_BL, AP_main::remember(), AP_main::revert(), and rootNode().
bool allBranchlengthsAreDefined  (  AP_tree_nlen *  tree  ) 
Definition at line 420 of file AP_tree_edge.cxx.
References allBranchlengthsAreDefined(), and AP_UNDEF_BL.
Referenced by allBranchlengthsAreDefined(), and AP_tree_edge::nni_rec().

inline 
Definition at line 431 of file AP_tree_edge.cxx.
References ap_main, AP_UNDEF_BL, AP_main::push_node(), and STRUCTURE.
Referenced by AP_tree_edge::nni_rec().
ostream& operator<<  (  std::ostream &  out, 
const AP_tree_edge *  e  
) 
Definition at line 572 of file AP_tree_edge.cxx.
const GBT_LEN AP_UNDEF_BL = 10.5 
Definition at line 363 of file AP_tree_edge.cxx.
Referenced by allBranchlengthsAreDefined(), undefine_branchlengths(), and update_undefined_leaf_branchlength().