tree_t Struct Reference

guide-tree structure More...

#include <muscle_tree.h>

Data Fields
uint	m_uNodeCount
uint	m_uCacheCount
uint *	m_uNeighbor1
uint *	m_uNeighbor2
uint *	m_uNeighbor3
bool *	m_bHasEdgeLength1
bool *	m_bHasEdgeLength2
bool *	m_bHasEdgeLength3
double *	m_dEdgeLength1
double *	m_dEdgeLength2
double *	m_dEdgeLength3
char **	m_ptrName
uint *	m_Ids
bool	m_bRooted
uint	m_uRootNodeIndex

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Detailed Description

guide-tree structure

Note:

We kept the original variable names here, to make it easy to search through Muscle's source code. From phy.cpp: Node has 0 to 3 neighbors: 0 neighbors: singleton root 1 neighbor: leaf, neighbor is parent 2 neigbors: non-singleton root 3 neighbors: internal node (other than root)

Minimal rooted tree is single node. Minimal unrooted tree is single edge. Leaf node always has nulls in neighbors 2 and 3, neighbor 1 is parent. When tree is rooted, neighbor 1=parent, 2=left, 3=right.

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Field Documentation

bool* tree_t::m_bHasEdgeLength1

bool* tree_t::m_bHasEdgeLength2

bool* tree_t::m_bHasEdgeLength3

bool tree_t::m_bRooted

tree is rooted

double* tree_t::m_dEdgeLength1

double* tree_t::m_dEdgeLength2

double* tree_t::m_dEdgeLength3

uint* tree_t::m_Ids

node id. index range: 0 -- m_uNodeCount

char** tree_t::m_ptrName

leaf labels. index range: 0 -- (m_uNodeCount+1)/2

uint tree_t::m_uCacheCount

reserved memory

uint* tree_t::m_uNeighbor1

parent node

uint* tree_t::m_uNeighbor2

left node

uint* tree_t::m_uNeighbor3

right node

uint tree_t::m_uNodeCount

number of nodes

uint tree_t::m_uRootNodeIndex

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The documentation for this struct was generated from the following file:

• src/clustal/muscle_tree.h