nexus_common.h File Reference

File handling functions for nexus format in general. More...

#include "char_vector.h"
#include "empirical_frequency.h"

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Macros
#define	MAX_NAME_LENGTH   4096
	maximum name length for taxa (alignment and tree files).

Functions
char_vector	new_char_vector_from_file (char *filename)
	General function that stores file content into char_vector_struct, removing shell-type comments.
char *	remove_nexus_comments (char **string, size_t *stringsize, FILE *stream)
	Removes (possible nested/multiline) nexus comments of the form [] (brackets).
char *	lowercase_string (char *string)
	Changes uppercase characters by lowercase versions.
char *	uppercase_string (char *string)
	Changes lowercase characters by uppercase versions.
char *	remove_space_from_string (char *string)
	Removes spaces, tabs from string.
bool	nonempty_string (char *string)
	returns bool::false if string is composed only of space characters (' ', ' ', '', '', etc).
bool	nonempty_fasta_line (char *string)
	returns bool::false if first nonspace character of string is ';' (FASTA comment) or '#' (HUPO extension)

Detailed Description

File handling functions for nexus format in general.