Classes | Functions | Variables
AP_tree_edge.cxx File Reference
#include "ap_tree_nlen.hxx"
#include "ap_main.hxx"
#include <AP_filter.hxx>
#include <arb_progress.h>
#include <cmath>
#include <iomanip>
Include dependency graph for AP_tree_edge.cxx:

Go to the source code of this file.


class  MutationsPerSite


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)


const GBT_LEN AP_UNDEF_BL = 10.5

Function Documentation

static void buildSonEdges ( AP_tree_nlen *  node)

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 double ap_calc_bootstrap_remark_sub ( int  seq_len,
const char old,
const char ne 

Definition at line 272 of file AP_tree_edge.cxx.

References diff(), GB_log_fak(), and max.

Referenced by ap_calc_bootstrap_remark().

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)

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.

Variable Documentation

const GBT_LEN AP_UNDEF_BL = 10.5