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

#include <Sequence/SingleSub.hpp>

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

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 45 of file SingleSub.hpp.

Member Function Documentation

◆ operator()()

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 55 of file SingleSub.cc.

◆ P0()

double Sequence::SingleSub::P0 ( void ) const

Returns: number of transitions at non-degenerate sites in the codon

Definition at line 69 of file SingleSub.cc.

◆ P2S()

double Sequence::SingleSub::P2S ( void ) const

Returns: number of transitions at transitional-degenerate sites in the codon

Definition at line 78 of file SingleSub.cc.

◆ P2V()

double Sequence::SingleSub::P2V ( void ) const

Returns: number of transitions at transversional-degenerate sites in the codon

Definition at line 87 of file SingleSub.cc.

◆ P4()

double Sequence::SingleSub::P4 ( void ) const

Returns: number of transitions at fourfold-degenerate sites in the codon

Definition at line 96 of file SingleSub.cc.

◆ Q0()

double Sequence::SingleSub::Q0 ( void ) const

Returns: number of transversions at non-degenerate sites in the codon

Definition at line 104 of file SingleSub.cc.

◆ Q2S()

double Sequence::SingleSub::Q2S ( void ) const

Returns: number of transversions at transitional-degenerate sites in the codon

Definition at line 113 of file SingleSub.cc.

◆ Q2V()

double Sequence::SingleSub::Q2V ( void ) const

Returns: number of transversions at transversional-degenerate sites in the codon

Definition at line 122 of file SingleSub.cc.

◆ Q4()

double Sequence::SingleSub::Q4 ( void ) const

Returns: number of transversions at fourfold-degenerate sites in the codon

Definition at line 131 of file SingleSub.cc.

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

Public Member Functions