biomcmc-lib  0.1
low level library for phylogenetic analysis
Macros | Functions
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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#define MAX_NAME_LENGTH   4096
 maximum name length for taxa (alignment and tree files).


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.