#include <utils.h>
#include <stdarg.h>
#include <utils_string.h>

Data Structures
struct	tagTree

struct	tagTreeNode

struct	tagPhylogenyNode

struct	tagMetapostConfig

Macros
#define	PS_SKIP_BL 0x1000

#define	PS_NWICK 0x0000

#define	PS_NHX 0x0FFE

#define	TREE_DEBUG 1

Typedefs
typedef struct tagTree *	pTree

typedef struct tagTreeNode *	pTreeNode

typedef struct tagTree	Tree

typedef struct tagTreeNode	TreeNode

typedef pTreeNode(*	tree_func_node_new )(pTree ptree)

typedef pTree(*	tree_func_new )(tree_func_node_new nfunc, int size)

typedef void(*	tree_func_node )(pTree ptree, pTreeNode pnode, va_list ap)

typedef void(*	tree_func_node_copy )(pTreeNode psrc, pTreeNode pdest)

typedef struct tagPhylogenyNode *	pPhylogenyNode

typedef struct tagPhylogenyNode	PhylogenyNode

typedef void(*	phylogeny_func_parse_node )(pTree ptree, pTreeNode pnode)

typedef void(*	phylogeny_func_name_modify )(pString str, pPhylogenyNode pnode)

typedef struct tagMetapostConfig *	pMetapostConfig

typedef double(*	metapost_remark )(pString str, pTree ptree, pMetapostConfig pmc, va_list ap)

typedef double(*	metapost_annotation_func )(pString str, pTreeNode pnode, pMetapostConfig pmc, va_list ap)

typedef struct tagMetapostConfig	MetapostConfig

Enumerations
enum	enumPhylogeny_speciation { PHYLOGENY_SPECIATION_NOT_DECIDED = 0, PHYLOGENY_SPECIATION_DUPLICATED, PHYLOGENY_SPECIATION_SPECIES }

enum	tagMPUnitList { MP_UNIT_IN = 0, MP_UNIT_MM, MP_UNIT_CM }

enum	tagMPDirectionList { MP_DIR_HORIZONTAL = 0, MP_DIR_VERTICAL }

enum	tagMPShapeList { MP_SHAPE_RECT = 1, MP_SHAPE_TRI = 2, MP_SHAPE_MASK = 3, MP_SHAPE_MOST_CENTER = 4, MP_SHAPE_LEAST_CENTER = 8 }

Functions
pTree	tree_new (tree_func_node_new nfunc, int size)

void	tree_new_fill (pTree ptree, tree_func_node_new nfunc)

void	tree_free (pTree ptree)

pTreeNode	tree_new_empty_node ()

int	tree_is_leaf (pTreeNode pnode)

int	tree_is_root (pTree ptree, pTreeNode pnode)

void	tree_add_child_to_node (pTreeNode parent, pTreeNode child)

void	tree_traveral_prefix (pTree ptree, tree_func_node func,...)

void	tree_traveral_postfix (pTree ptree, tree_func_node func,...)

void	tree_traveral_infix (pTree ptree, tree_func_node func,...)

void	tree_clear_reg (pTree ptree)

void *	tree_get_child (pTreeNode ptnode, int idx)

pTree	tree_copy (pTree psrc, tree_func_node_new new_node_func, tree_func_node_copy copy)

void	tree_build_node_list (pTree ptree)

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

pString	phylogeny_string (pTree ptree, phylogeny_func_name_modify fmod)

void	phylogeny_node_copy (pTreeNode psrc, pTreeNode pdest)

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,...)

pTree	phylogeny_load_from_file (char *sztree, tree_func_new new_tree_func, tree_func_node_new new_tree_node_func, phylogeny_func_parse_node parsefunc)

void	phylogeny_free (pTree ptree)

pTreeNode	phylogeny_new_empty_node (pTree ptree)

void	phylogeny_clear_node (pPhylogenyNode pnode)

pTree	phylogeny_copy (pTree psrc)

pTree	phylogeny_new (char *sztree, phylogeny_func_parse_node parsefunc)

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)

pTreeNode	phylogeny_get_sibling (pTree ptree, pTreeNode ptnode)

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

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

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

Macro Definition Documentation

#define PS_NHX 0x0FFE

#define PS_NWICK 0x0000

#define PS_SKIP_BL 0x1000

#define TREE_DEBUG 1

Typedef Documentation

typedef double(* metapost_annotation_func)(pString str, pTreeNode pnode, pMetapostConfig pmc, va_list ap)

typedef double(* metapost_remark)(pString str, pTree ptree, pMetapostConfig pmc, va_list ap)

typedef struct tagMetapostConfig MetapostConfig

typedef void(* phylogeny_func_name_modify)(pString str, pPhylogenyNode pnode)

typedef void(* phylogeny_func_parse_node)(pTree ptree, pTreeNode pnode)

typedef struct tagPhylogenyNode PhylogenyNode

typedef struct tagMetapostConfig* pMetapostConfig

typedef struct tagPhylogenyNode* pPhylogenyNode

typedef struct tagTree* pTree

typedef struct tagTreeNode* pTreeNode

typedef struct tagTree Tree

typedef pTree(* tree_func_new)(tree_func_node_new nfunc, int size)

typedef void(* tree_func_node)(pTree ptree, pTreeNode pnode, va_list ap)

typedef void(* tree_func_node_copy)(pTreeNode psrc, pTreeNode pdest)

typedef pTreeNode(* tree_func_node_new)(pTree ptree)

typedef struct tagTreeNode TreeNode

Simple structure representing a generic node in a generic tree. Has an ID and pointers to parent and children. Implementers of tree_func_node_new are expected to return a value that can be cast to this structure.

Enumeration Type Documentation

enum enumPhylogeny_speciation

Enumerator
PHYLOGENY_SPECIATION_NOT_DECIDED
PHYLOGENY_SPECIATION_DUPLICATED
PHYLOGENY_SPECIATION_SPECIES

enum tagMPDirectionList

Enumerator
MP_DIR_HORIZONTAL
MP_DIR_VERTICAL

enum tagMPShapeList

Enumerator
MP_SHAPE_RECT
MP_SHAPE_TRI
MP_SHAPE_MASK
MP_SHAPE_MOST_CENTER
MP_SHAPE_LEAST_CENTER

enum tagMPUnitList

Enumerator
MP_UNIT_IN
MP_UNIT_MM
MP_UNIT_CM

Function Documentation

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
	)

pTree phylogeny_load_from_file	(	char *	sztree,
		tree_func_new	new_tree_func,
		tree_func_node_new	new_tree_node_func,
		phylogeny_func_parse_node	parsefunc
	)

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,
			...
	)

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,
			...
	)

void tree_add_child_to_node	(	pTreeNode	parent,
		pTreeNode	child
	)

void tree_build_node_list ( pTree ptree )

void tree_clear_reg ( pTree ptree )

pTree tree_copy	(	pTree	psrc,
		tree_func_node_new	new_node_func,
		tree_func_node_copy	copy
	)

void tree_free ( pTree ptree )

void* tree_get_child	(	pTreeNode	ptnode,
		int	idx
	)

int tree_is_leaf ( pTreeNode pnode )

int tree_is_root	(	pTree	ptree,
		pTreeNode	pnode
	)

pTree tree_new	(	tree_func_node_new	nfunc,
		int	size
	)

pTreeNode tree_new_empty_node ( )

void tree_new_fill	(	pTree	ptree,
		tree_func_node_new	nfunc
	)

void tree_traveral_infix	(	pTree	ptree,
		tree_func_node	func,
			...
	)

void tree_traveral_postfix	(	pTree	ptree,
		tree_func_node	func,
			...
	)

void tree_traveral_prefix	(	pTree	ptree,
		tree_func_node	func,
			...
	)

Data Structures

Macros

Typedefs

Enumerations

Functions

Macro Definition Documentation

Typedef Documentation

Enumeration Type Documentation

Function Documentation