phylogeny.c File Reference

#include "../config.h"
#include "tree.h"
#include <string.h>
#include <stdlib.h>
#include <sys/types.h>
#include <utils.h>
#include <utils_string.h>
#include "memalloc.h"
#include <unistd.h>
#include <strings.h>

Data Structures
struct	PnodeParam

Typedefs
typedef PnodeParam *	pPnodeParam

Functions
void	phylogeny_clear_node (pPhylogenyNode pnode)
pTreeNode	phylogeny_new_empty_node (pTree ptree)
void	phylogeny_node_copy (pTreeNode psrc, pTreeNode pdest)
size_t	__phylogeny_string_cmp (const void *arg1, const void *arg2)
int	phylogeny_set_node (pTree ptree, pTreeNode ptnode, pPnodeParam param)
void	__phylogeny_free_node (pTree ptree, pTreeNode ptnode, va_list ap1)
void	phylogeny_free (pTree ptree)
char *	phylogeny_interpret_node (pTree ptree, pTreeNode ptnode, char *sztree)
int	phylogeny_check_tree_string (char *sztree)
pTree	phylogeny_load_from_string (char *sztree, tree_func_new new_tree_func, tree_func_node_new new_tree_node_func, phylogeny_func_parse_node parsefunc, int size)
pTree	phylogeny_root_tree (pTree ptree, tree_func_node_new new_tree_node_func, phylogeny_func_parse_node parsefunc,...)
void	__phylogeny_string (pString pstr, pPhylogenyNode pnode, phylogeny_func_name_modify fmod)
pString	phylogeny_string_newick (pTree ptree, phylogeny_func_name_modify fmod, int opts)
pString	phylogeny_string_nhx (pTree ptree, phylogeny_func_name_modify fmod, int opts)
pString	phylogeny_string (pTree ptree, phylogeny_func_name_modify fmod)
pTree	phylogeny_new (char *sztree, phylogeny_func_parse_node parsefunc)
pTree	phylogeny_copy (pTree psrc)
pTreeNode	phylogeny_get_sibling (pTree ptree, pTreeNode ptnode)
pTree	phylogeny_split_tree (pTree ptree, int idx, tree_func_node freenode)
void	__phylogeny_delete_nodes (pTree ptree, pTreeNode pnode, tree_func_node freenode)
int	phylogeny_delete_nodes_by_index (pTree ptree, int idx, tree_func_node freenode)
int	phylogeny_delete_nodes_by_reg (pTree ptree, tree_func_node freenode)
int	phylogeny_delete_nodes_by_func (pTree ptree, tree_func_node filter, tree_func_node freenode)
void	phylogeny_increase_branchlength (pTree ptree, int idx)
void	phylogeny_add_branchlength (pTree ptree, int idx, int add)
pString	phylogeny_to_mp (pTree ptree, pMetapostConfig pmc,...)

Typedef Documentation

typedef PnodeParam* pPnodeParam

Function Documentation

void __phylogeny_delete_nodes	(	pTree	ptree,
		pTreeNode	pnode,
		tree_func_node	freenode
	)

void __phylogeny_free_node	(	pTree	ptree,
		pTreeNode	ptnode,
		va_list	ap1
	)

void __phylogeny_string	(	pString	pstr,
		pPhylogenyNode	pnode,
		phylogeny_func_name_modify	fmod
	)

size_t __phylogeny_string_cmp	(	const void *	arg1,
		const void *	arg2
	)

void phylogeny_add_branchlength	(	pTree	ptree,
		int	idx,
		int	add
	)

int phylogeny_check_tree_string

(

char *

sztree

)

void phylogeny_clear_node

(

pPhylogenyNode

pnode

)

pTree phylogeny_copy

(

pTree

psrc

)

int phylogeny_delete_nodes_by_func	(	pTree	ptree,
		tree_func_node	filter,
		tree_func_node	freenode
	)

int phylogeny_delete_nodes_by_index	(	pTree	ptree,
		int	idx,
		tree_func_node	freenode
	)

int phylogeny_delete_nodes_by_reg	(	pTree	ptree,
		tree_func_node	freenode
	)

void phylogeny_free

(

pTree

ptree

)

pTreeNode phylogeny_get_sibling	(	pTree	ptree,
		pTreeNode	ptnode
	)

void phylogeny_increase_branchlength	(	pTree	ptree,
		int	idx
	)

char* phylogeny_interpret_node	(	pTree	ptree,
		pTreeNode	ptnode,
		char *	sztree
	)

pTree phylogeny_load_from_string	(	char *	sztree,
		tree_func_new	new_tree_func,
		tree_func_node_new	new_tree_node_func,
		phylogeny_func_parse_node	parsefunc,
		int	size
	)

pTree phylogeny_new	(	char *	sztree,
		phylogeny_func_parse_node	parsefunc
	)

pTreeNode phylogeny_new_empty_node

(

pTree

ptree

)

void phylogeny_node_copy	(	pTreeNode	psrc,
		pTreeNode	pdest
	)

pTree phylogeny_root_tree	(	pTree	ptree,
		tree_func_node_new	new_tree_node_func,
		phylogeny_func_parse_node	parsefunc,
			...
	)

int phylogeny_set_node	(	pTree	ptree,
		pTreeNode	ptnode,
		pPnodeParam	param
	)

pTree phylogeny_split_tree	(	pTree	ptree,
		int	idx,
		tree_func_node	freenode
	)

pString phylogeny_string	(	pTree	ptree,
		phylogeny_func_name_modify	fmod
	)

pString phylogeny_string_newick	(	pTree	ptree,
		phylogeny_func_name_modify	fmod,
		int	opts
	)

pString phylogeny_string_nhx	(	pTree	ptree,
		phylogeny_func_name_modify	fmod,
		int	opts
	)

pString phylogeny_to_mp	(	pTree	ptree,
		pMetapostConfig	pmc,
			...
	)