muscle_tree.h File Reference

#include <stdio.h>
#include "util.h"

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Data Structures
struct	tree_t
	guide-tree structure More...

Typedefs
typedef unsigned int	uint

Functions
void	MuscleTreeCreate (tree_t *tree, uint uLeafCount, uint uRoot, const uint *Left, const uint *Right, const float *LeftLength, const float *RightLength, const uint *LeafIds, char **LeafNames)
	create a muscle tree More...
void	MuscleTreeToFile (FILE *fp, tree_t *tree)
	write a muscle tree to a file in newick format (distances and all names) More...
int	MuscleTreeFromFile (tree_t *tree, char *ftree)
void	FreeMuscleTree (tree_t *tree)
void	LogTree (tree_t *tree, FILE *fp)
bool	IsRooted (tree_t *tree)
	check if tree is a rooted tree More...
uint	GetNodeCount (tree_t *tree)
uint	GetLeafCount (tree_t *tree)
uint	FirstDepthFirstNode (tree_t *tree)
	returns first leaf node for a depth-first traversal of tree More...
uint	NextDepthFirstNode (uint nodeindex, tree_t *tree)
	returns next leaf node index for depth-first traversal of tree More...
bool	IsLeaf (uint nodeindex, tree_t *tree)
	check if given node is a leaf node More...
void	SetLeafId (tree_t *tree, uint uNodeIndex, uint uId)
uint	GetLeafId (uint nodeindex, tree_t *tree)
char *	GetLeafName (unsigned uNodeIndex, tree_t *tree)
uint	GetLeft (uint nodeindex, tree_t *tree)
uint	GetRight (uint nodeindex, tree_t *tree)
uint	GetRootNodeIndex (tree_t *tree)
bool	IsRoot (uint uNodeIndex, tree_t *tree)