tree_t Struct Reference

guide-tree structure More...

#include <muscle_tree.h>

Data Fields

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

Detailed Description

guide-tree structure

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

tree is rooted

node id. index range: 0 -- m_uNodeCount

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

reserved memory

parent node

left node

right node

number of nodes

The documentation for this struct was generated from the following file:
Generated on Fri Aug 31 05:32:52 2012 for Clustal Omega by  doxygen 1.6.3