topology_space.h File Reference

Reads tree files in nexus format and creates a vector of topologies. More...

#include "newick_space.h"

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Data Structures
struct	topology_space_struct
	Collection of topologies from tree file. When topologies have no branch lengths we store only unique topologies. More...

Typedefs
typedef struct topology_space_struct *	topology_space

Functions
void	add_string_with_size_to_topology_space (topology_space *tsp_address, char *long_string, size_t string_size, bool use_root_location)
	Read tree in newick format until char string_size, returning updated topolgy_space. Auxiliary for python module. More...
void	add_topology_to_topology_space_if_distinct (topology topol, topology_space tsp, double tree_weight, bool use_root_location)
	Add topology to topology_space only if unrooted version is distinct, updating freqs, trees[] etc. Aux for python module.
topology_space	read_topology_space_from_file (char *seqfilename, hashtable external_taxhash, bool use_root_location)
	Read tree file and store info in topology_space_struct with possible external hashtable to impose the leaf ordering.
topology_space	read_topology_space_from_file_with_burnin_thin (char *seqfilename, hashtable external_taxhash, int burnin, int thin, bool use_root_location)
	lower level function where we can specify burnin and thinning factor, in iterations
void	merge_topology_spaces (topology_space ts1, topology_space ts2, double weight_ts1, bool use_root_location)
	merge trees from two topology_space objects, assuming names hashtable is the same
void	sort_topology_space_by_frequency (topology_space tsp, double *external_freqs)
void	save_topology_space_to_trprobs_file (topology_space tsp, char *filename, double credible)
	Save topology_space to a file, in format nexus w/ trprobs, up to "credible" cummul frequency.
int	estimate_treesize_from_file (char *seqfilename)
	Quickly counts the number of leaves in a tree file, without storing any info. Assumes file and trees are well-formed.
topology_space	new_topology_space (void)
	Allocates memory for topology_space_struct (set of trees present in nexus file).
void	del_topology_space (topology_space tsp)
	Free memory from topology_space_struct.

Detailed Description

Reads tree files in nexus format and creates a vector of topologies.

The topology_space_struct is distinct from the newick_space_struct since all trees here must share same char_vector (newick spaces can have general, uncomparable trees), and also since we store the distribution of trees (that is, each tree will have a frequency/representativity associated to it, as typical from Bayesian analyes).

Function Documentation

add_string_with_size_to_topology_space()

void add_string_with_size_to_topology_space	(	topology_space *	tsp,
		char *	long_string,
		size_t	string_size,
		bool	use_root_location
	)

Read tree in newick format until char string_size, returning updated topolgy_space. Auxiliary for python module.

Read tree in newick format until char string_size, returning updated topolgy_space. Auxiliary for python module.