Sequence::SingleSub Class Reference
[Classes related to the calculation of Ka and Ks]

Deal with codons differing at 1 position. More...

#include <Sequence/SingleSub.hpp>

List of all members.

Public Member Functions
void	operator() (const RedundancyCom95 *sitesObj, const std::string &cod1, const std::string &cod2)
double	P0 (void) const
double	P2S (void) const
double	P2V (void) const
double	P4 (void) const
double	Q0 (void) const
double	Q2S (void) const
double	Q2V (void) const
double	Q4 (void) const

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Detailed Description

Deal with codons differing at 1 position.

A functor to obtain divergence statistics for Comeron's method for codons that differ at one position. Used by Sequence::Comeron95

Author:

Kevin Thornton

Definition at line 44 of file SingleSub.hpp.

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Member Function Documentation

void Sequence::SingleSub::operator()	(	const RedundancyCom95 *	sitesObj,
		const std::string &	cod1,
		const std::string &	cod2
	)

Parameters:

	sitesObj	an object of type Sequence::RedundancyCom95
	cod1	a std::string of length 3 representing a codon
	cod2	a std::string of length 3 representing a codon

Note:

cod1 and cod2 lengths are verified by assert()

Definition at line 32 of file SingleSub.cc.

double Sequence::SingleSub::P0

(

void

)

const

Returns:

number of transitions at non-degenerate sites in the codon

Definition at line 48 of file SingleSub.cc.

double Sequence::SingleSub::P2S

(

void

)

const

Returns:

number of transitions at transitional-degenerate sites in the codon

Definition at line 57 of file SingleSub.cc.

double Sequence::SingleSub::P2V

(

void

)

const

Returns:

number of transitions at transversional-degenerate sites in the codon

Definition at line 66 of file SingleSub.cc.

double Sequence::SingleSub::P4

(

void

)

const

Returns:

number of transitions at fourfold-degenerate sites in the codon

Definition at line 75 of file SingleSub.cc.

double Sequence::SingleSub::Q0

(

void

)

const

Returns:

number of transversions at non-degenerate sites in the codon

Definition at line 83 of file SingleSub.cc.

double Sequence::SingleSub::Q2S

(

void

)

const

Returns:

number of transversions at transitional-degenerate sites in the codon

Definition at line 92 of file SingleSub.cc.

double Sequence::SingleSub::Q2V

(

void

)

const

Returns:

number of transversions at transversional-degenerate sites in the codon

Definition at line 101 of file SingleSub.cc.

double Sequence::SingleSub::Q4

(

void

)

const

Returns:

number of transversions at fourfold-degenerate sites in the codon

Definition at line 110 of file SingleSub.cc.

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

• SingleSub.hpp
• SingleSub.cc