ARB
Classes | Typedefs | Functions
AP_Tree.cxx File Reference
#include "AP_Tree.hxx"
#include "AP_TreeShader.hxx"
#include <AP_filter.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <arb_str.h>
#include <ad_cb.h>
#include <math.h>
#include <map>
#include <climits>
#include <algorithm>
Include dependency graph for AP_Tree.cxx:

Go to the source code of this file.

Classes

class  AP_DefaultTreeShader
 
class  ValueCounter< T >
 
class  LongBranchMarker
 
struct  DepthMarker
 
class  DistanceCounter
 
class  EdgeDistances
 

Typedefs

typedef ValueCounter< double > Distance
 

Functions

static void ap_tree_node_deleted (GBDATA *, AP_tree *tree)
 
int tree_read_byte (GBDATA *tree, const char *key, int init)
 
float tree_read_float (GBDATA *tree, const char *key, float init)
 
static GB_ERROR tree_write_byte (GBDATA *gb_tree, AP_tree *node, short i, const char *key, int init)
 
static GB_ERROR tree_write_float (GBDATA *gb_tree, AP_tree *node, float f, const char *key, float init)
 
GBDATAfind_group_name_entry (TreeNode *node)
 
template<typename T >
ValueCounter< Toperator+ (const ValueCounter< T > &c1, const ValueCounter< T > &c2)
 
template<typename T >
ValueCounter< Toperator+ (const ValueCounter< T > &c, const T &inc)
 
static int ap_mark_degenerated (AP_tree *at, double degeneration_factor, double &max_degeneration)
 
static int ap_mark_duplicates_rek (AP_tree *at, GB_HASH *seen_species)
 
static double ap_just_tree_rek (AP_tree *at)
 
static void relink_tree_rek (AP_tree *node, void(*relinker)(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash), GB_HASH *organism_hash)
 

Typedef Documentation

typedef ValueCounter<double> Distance

Definition at line 1315 of file AP_Tree.cxx.

Function Documentation

static void ap_tree_node_deleted ( GBDATA ,
AP_tree tree 
)
static

AP_tree **********

Definition at line 138 of file AP_Tree.cxx.

References TreeNode::gb_node, and NULp.

Referenced by AP_tree::~AP_tree().

int tree_read_byte ( GBDATA tree,
const char key,
int  init 
)
inline

Definition at line 426 of file AP_Tree.cxx.

References GB_entry(), GB_read_byte(), and init.

float tree_read_float ( GBDATA tree,
const char key,
float  init 
)
inline

Definition at line 434 of file AP_Tree.cxx.

References GB_entry(), GB_read_float(), and init.

static GB_ERROR tree_write_byte ( GBDATA gb_tree,
AP_tree node,
short  i,
const char key,
int  init 
)
static
static GB_ERROR tree_write_float ( GBDATA gb_tree,
AP_tree node,
float  f,
const char key,
float  init 
)
static
GBDATA* find_group_name_entry ( TreeNode node)
inline

Definition at line 573 of file AP_Tree.cxx.

References GB_entry(), TreeNode::gb_node, TreeNode::has_group_info(), and NULp.

Referenced by AP_tree::move_group_to().

template<typename T >
ValueCounter<T> operator+ ( const ValueCounter< T > &  c1,
const ValueCounter< T > &  c2 
)
inline

Definition at line 1053 of file AP_Tree.cxx.

template<typename T >
ValueCounter<T> operator+ ( const ValueCounter< T > &  c,
const T inc 
)
inline

Definition at line 1057 of file AP_Tree.cxx.

static int ap_mark_degenerated ( AP_tree at,
double  degeneration_factor,
double &  max_degeneration 
)
static

Definition at line 1465 of file AP_Tree.cxx.

References TreeNode::is_leaf(), and ARB_seqtree::mark_subtree().

Referenced by AP_tree::mark_degenerated_branches().

static int ap_mark_duplicates_rek ( AP_tree at,
GB_HASH seen_species 
)
static
static double ap_just_tree_rek ( AP_tree at)
static
static void relink_tree_rek ( AP_tree node,
void(*)(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash)  relinker,
GB_HASH organism_hash 
)
static

Definition at line 1565 of file AP_Tree.cxx.

References TreeNode::gb_node, TreeNode::is_leaf(), and TreeNode::name.

Referenced by AP_tree::relink_tree().