Main Page   Modules   Namespace List   Class Hierarchy   Compound List   File List   Namespace Members   Compound Members   Examples  

bioinfo::bio_bit_traits Class Template Reference

"char_traits" specification for bit encoded bio sequence characters. More...

#include <bio_bit_traits.h>

Inheritance diagram for bioinfo::bio_bit_traits:

Inheritance graph
[legend]
Collaboration diagram for bioinfo::bio_bit_traits:

Collaboration graph
[legend]
List of all members.

Public Types

typedef std::char_traits<std::bitset<
NB> >::char_type 
char_type
typedef std::char_traits<char>::char_type basic_char_type

Static Public Methods

std::size_t bit_size ()
basic_char_type char_code (char_type)
std::size_t bit_code (basic_char_type)
bool valid_code (basic_char_type)

Detailed Description

template<size_t NB> class bioinfo::bio_bit_traits

"char_traits" specification for bit encoded bio sequence characters.

The type of characters expected are either nucleic acid codes or amino acid codes. Code sizes are expected to vary depending on the application. The initial case defaults to the case where only 4 character codes are used: adenine,cytosine,guanine,thymine. template parameter NB defines the number of bits per character.


Member Typedef Documentation

template<size_t NB>
typedef std::char_traits< char >::char_type bioinfo::bio_bit_traits<NB>::basic_char_type<char>
 

reference to char type

template<size_t NB>
typedef std::char_traits< std::bitset< NB > >::char_type bioinfo::bio_bit_traits<NB>::char_type<std::bitset<NB> >
 

single character type


Member Function Documentation

template<size_t NB>
std::size_t bioinfo::bio_bit_traits< NB >::bit_code ( basic_char_type c ) [inline, static]
 

Parameters:
basic_char_type   single character (ascii code)
Returns:
custom bit encoding of single character

template<size_t NB>
std::size_t bioinfo::bio_bit_traits<NB>::bit_size ( ) [inline, static]
 

Returns:
number of bits used to encode a single nucleic acid character

template<size_t NB>
basic_char_type bioinfo::bio_bit_traits<NB>::char_code ( char_type ) [inline, static]
 

Parameters:
char_type   = single character of sequence
Returns:
single character code defined by right most bit_size() bits in char_type
See also:
bit_size()

template<size_t NB>
bool bioinfo::bio_bit_traits< NB >::valid_code ( basic_char_type c ) [inline, static]
 

Parameters:
basic_char_type   = single character
Returns:
true if basic_char_type is recognized


The documentation for this class was generated from the following files: