nucleotide_index.hpp File Reference

#include "boost/algorithm/string/predicate_facade.hpp"
#include "boost/assert.hpp"
#include "boost/multi_array.hpp"
#include "vdj_pipe/detail/disable_warnings.hpp"
#include "vdj_pipe/exception.hpp"

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Classes
struct	vdj_pipe::Is_ambiguous

Namespaces
	vdj_pipe
	Main namespace of vdj_pipe library.
	vdj_pipe::detail

Macros
#define	VDJ_PIPE_N_NUCLEOTIDES   16

Typedefs
typedef boost::multi_array< int, 2 >	vdj_pipe::scoring_matrix_t

Enumerations
enum	vdj_pipe::Nucleotide {   vdj_pipe::Adenine = 0, vdj_pipe::Cytosine = 1, vdj_pipe::Guanine = 2, vdj_pipe::Thymine = 3,   vdj_pipe::Any = 4, vdj_pipe::Uracil = 5, vdj_pipe::Purine = 6, vdj_pipe::Pyrimidine = 7,   vdj_pipe::Ketone = 8, vdj_pipe::Amine = 9, vdj_pipe::Strong = 10, vdj_pipe::Weak = 11,   vdj_pipe::not_A = 12, vdj_pipe::not_C = 13, vdj_pipe::not_G = 14, vdj_pipe::not_T = 15 }

Functions
Nucleotide	vdj_pipe::nucleotide_index (const char c)
bool	vdj_pipe::is_ambiguous (const char c)
Nucleotide	vdj_pipe::complement (const Nucleotide n)
char	vdj_pipe::complement (const char c)
char	vdj_pipe::to_capital (const Nucleotide n)
char	vdj_pipe::to_small (const Nucleotide n)
template<int A, int I, int P, int U>
scoring_matrix_t	vdj_pipe::detail::make_sm ()
template<int Match, int Mismatch, int Approximate, int Uncertain>
scoring_matrix_t const &	vdj_pipe::scoring_matrix ()
int	vdj_pipe::identity (const Nucleotide n1, const Nucleotide n2, scoring_matrix_t const &sm=scoring_matrix< 2,-2, 1, 0 >())

Detailed Description

part of vdj_pipe project.

Distributed under GNU General Public License, Version 3; see doc/license.txt.
Copyright Mikhail K Levin 2013

Macro Definition Documentation

#define VDJ_PIPE_N_NUCLEOTIDES   16