Clustal Omega  1.2.4
Data Fields
tree_t Struct Reference

guide-tree structure More...

#include <muscle_tree.h>

Data Fields

uint m_uNodeCount
 
uint m_uCacheCount
 
uintm_uNeighbor1
 
uintm_uNeighbor2
 
uintm_uNeighbor3
 
bool * m_bHasEdgeLength1
 
bool * m_bHasEdgeLength2
 
bool * m_bHasEdgeLength3
 
double * m_dEdgeLength1
 
double * m_dEdgeLength2
 
double * m_dEdgeLength3
 
char ** m_ptrName
 
uintm_Ids
 
bool m_bRooted
 
uint m_uRootNodeIndex
 

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.

Field Documentation

§ m_bHasEdgeLength1

bool* tree_t::m_bHasEdgeLength1

§ m_bHasEdgeLength2

bool* tree_t::m_bHasEdgeLength2

§ m_bHasEdgeLength3

bool* tree_t::m_bHasEdgeLength3

§ m_bRooted

bool tree_t::m_bRooted

tree is rooted

§ m_dEdgeLength1

double* tree_t::m_dEdgeLength1

§ m_dEdgeLength2

double* tree_t::m_dEdgeLength2

§ m_dEdgeLength3

double* tree_t::m_dEdgeLength3

§ m_Ids

uint* tree_t::m_Ids

node id. index range: 0 – m_uNodeCount

§ m_ptrName

char** tree_t::m_ptrName

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

§ m_uCacheCount

uint tree_t::m_uCacheCount

reserved memory

§ m_uNeighbor1

uint* tree_t::m_uNeighbor1

parent node

§ m_uNeighbor2

uint* tree_t::m_uNeighbor2

left node

§ m_uNeighbor3

uint* tree_t::m_uNeighbor3

right node

§ m_uNodeCount

uint tree_t::m_uNodeCount

number of nodes

§ m_uRootNodeIndex

uint tree_t::m_uRootNodeIndex

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