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)
GBDATA *	find_group_name_entry (TreeNode *node)
template<typename T >
ValueCounter< T >	operator+ (const ValueCounter< T > &c1, const ValueCounter< T > &c2)
template<typename T >
ValueCounter< T >	operator+ (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

Definition at line 469 of file AP_Tree.cxx.

References error(), GB_BYTE, GB_create(), GB_create_container(), GB_delete(), GB_entry(), TreeNode::gb_node, GB_write_byte(), and NULp.

Referenced by AP_tree::tree_write_tree_rek().

static GB_ERROR tree_write_float ( GBDATA *  gb_tree, AP_tree *  node, float  f, const char *  key, float  init  )

static

Definition at line 502 of file AP_Tree.cxx.

References error(), GB_await_error(), GB_create_container(), GB_delete(), GB_entry(), TreeNode::gb_node, GBT_write_float(), and NULp.

Referenced by AP_tree::tree_write_tree_rek().

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

Definition at line 1506 of file AP_Tree.cxx.

References TreeNode::gb_node, GB_write_flag(), GBS_read_hash(), GBS_write_hash(), TreeNode::is_leaf(), and TreeNode::name.

Referenced by AP_tree::mark_duplicates().

static double ap_just_tree_rek ( AP_tree *  at )

static

Definition at line 1540 of file AP_Tree.cxx.

References diff(), TreeNode::is_leaf(), TreeNode::leftlen, and TreeNode::rightlen.

Referenced by AP_tree::justify_branch_lenghs().

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().