Data from alignment file. More...

#include <alignment.h>

Collaboration diagram for alignment_struct:

Data Fields
int	ntax

int	nchar

int	npat

char_vector	character
	Number of species, sites and patterns according to sequence file.

char_vector	taxlabel
	Vector with aligned sequence for each taxon.

char_vector	taxshort
	Taxon names from file.

hashtable	taxlabel_hash
	Alias (short version) for taxon names that can be used in newick trees.

int	n_charset
	Lookup table with taxon names.

int *	charset_start
	Number of gene segments (ASSUMPTIONS BLOCK).

int *	charset_end

bool	is_aligned
	Start and end of each gene segment (from 1...NCHAR) (ASSUMPTIONS ).

int *	site_pattern
	FASTA files don't need to be aligned; NEXUS files do.

int *	pattern_freq
	pattern, in alignment_struct::character, to which original site belongs.

char *	filename
	if sequences are aligned, this is the frequency of each pattern.

int	ref_counter
	name of the original file, with extension removed

Detailed Description

Data from alignment file.

The documentation for this struct was generated from the following file:

Data Fields