ARB
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#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>
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 ValueCounter<double> Distance |
Definition at line 1315 of file AP_Tree.cxx.
AP_tree **********
Definition at line 138 of file AP_Tree.cxx.
References TreeNode::gb_node, and NULp.
Referenced by AP_tree::~AP_tree().
Definition at line 426 of file AP_Tree.cxx.
References GB_entry(), GB_read_byte(), and init.
Definition at line 434 of file AP_Tree.cxx.
References GB_entry(), GB_read_float(), and init.
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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().
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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().
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().
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Definition at line 1053 of file AP_Tree.cxx.
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inline |
Definition at line 1057 of file AP_Tree.cxx.
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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().
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().
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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().
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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().