theplu::yat::omic::DNA Class Reference

#include <yat/omic/DNA.h>

Inheritance diagram for theplu::yat::omic::DNA:

Public Member Functions
	DNA (void)
	Default Constructor. More...
	DNA (const DNA &)
	Copy Constructor.
	DNA (char c)
DNA	complement (void) const
char	get (void) const
DNA &	operator&= (const DNA &rhs)
DNA &	operator|= (const DNA &rhs)
DNA &	operator^= (const DNA &rhs)
DNA &	operator= (char c)
	assign from a char More...

Friends
bool	operator== (const DNA &, const DNA &)

Related Functions
(Note that these are not member functions.)
std::string	expand (const DNA &)
bool	operator== (const DNA &lhs, const DNA &rhs)
std::ostream &	operator<< (std::ostream &os, const DNA &dna)

Detailed Description

Class for DNA e.g. A, C, G, or T. Nucleotides can be overloaded e.g. 'A' | 'G' == 'R'. Null object (opposite to 'N') is denoted by space, ' '.

A	A
T	T
G	G
C	C
R	G or A
Y	T or C
M	A or C
K	G or T
S	G or C
W	A or T
H	A or C or T
B	G or T or C
V	G or C or A
D	G or T or A
N	A or C or T or G
' '	none

Since

New in yat 0.7

Constructor & Destructor Documentation

theplu::yat::omic::DNA::DNA

(

void

)

Default Constructor.

Equivalent to DNA(' ').

theplu::yat::omic::DNA::DNA ( char  c )

explicit

Parameters

c	must be one of the following 16 characters, A, C, G, T, M, R, W, S, Y, K, B, D, H, V, N, or ' '.

Exceptions

std::invalid_argument

if c is not one of 16 allowed characters

Member Function Documentation

DNA theplu::yat::omic::DNA::complement

(

void

)

const

Calculates complement, i.e., 'A' becomes 'T' and 'G' becomes 'C' etc. In case of combination the returned DNA will be the combination of all complements, i.e., 'R' becomes 'Y.

Returns

Complementary base

char theplu::yat::omic::DNA::get

(

void

)

const

Returns

DNA as a character

DNA& theplu::yat::omic::DNA::operator&=

(

const DNA &

rhs

)

Modifies lhs and keeps those bases present on both sides, i.e., if lhs, for example, is 'R' and rhs is 'M' the overlap is 'A' so resulting lhs will be an 'A'.

As DNA inherits boost::operators<DNA> corresponding operator&(const DNA&, const DNA&) is also available.

DNA& theplu::yat::omic::DNA::operator=

(

char

c

)

assign from a char

Returns

resulting DNA

Since

New in yat 0.8

DNA& theplu::yat::omic::DNA::operator^=

(

const DNA &

rhs

)

Modifies lhs to a combination of bases that are present on one side (not both). If, for example, lhs is 'M' and rhs is 'A', resulting lhs will be 'C'.

As DNA inherits boost::operators<DNA> corresponding operator^(const DNA&, const DNA&) is also available.

DNA& theplu::yat::omic::DNA::operator|=

(

const DNA &

rhs

)

Modifies lhs to a combination of bases present on either side. If, for example, lhs is 'A' and rhs is 'C', resuting lhs will be 'M'.

As DNA inherits boost::operators<DNA> corresponding operator|(const DNA&, const DNA&) is also available.

Friends And Related Function Documentation

std::string expand ( const DNA &  )

related

Returns

a string of combinations of A, C, G, and T.

Since

New in yat 0.7

std::ostream & operator<< ( std::ostream &  os, const DNA &  dna  )

related

Outputs the DNA to os. Equivalent to os << dna.get().

Since

New in yat 0.7

bool operator== ( const DNA &  lhs, const DNA &  rhs  )

related

Returns

true if bases are the same, i.e., equivalent to lhs.get()==rhs.get()

As DNA is inherits boost::operators<DNA> corresponding operator!=(const DNA&, const DNA&) is also available.

Since

New in yat 0.7

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

• yat/omic/DNA.h