Deal with codons differing at all 3 positions. More...

#include <Sequence/ThreeSubs.hpp>

Public Member Functions
void	operator() (const RedundancyCom95 &sitesObj, const std::string &codon1, const std::string &codon2, const Sequence::WeightingScheme3 *weights3)

	~ThreeSubs (void)

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 all 3 positions.

Pathways when codons differ at 3 sites

A function object to obtain divergence statistics for Comeron's method for codons that differ at three positions. Alternate paths are weighted by Grantham's distances. Used by Sequence::Comeron95

Note: You really need to study the above figure if you want to implement your own scheme to weight these pathways (done by deriving a class from Sequence::WeightingScheme3), you must know how this class names and assigns the intermediate steps and the branches. In other words, you must study the implementation of this class. You may also want to refer to the implementations of Sequence::GranthamWeights3 for an example of implementing weighting schemes.

Definition at line 52 of file ThreeSubs.hpp.

Constructor & Destructor Documentation

◆ ~ThreeSubs()

Sequence::ThreeSubs::~ThreeSubs ( void )

does nothing

Definition at line 53 of file ThreeSubs.cc.

Member Function Documentation

◆ operator()()

void Sequence::ThreeSubs::operator()	(	const RedundancyCom95 &	sitesObj,
		const std::string &	codon1,
		const std::string &	codon2,
		const Sequence::WeightingScheme3 *	weights3
	)

Parameters

sitesObj	an object of type Sequence::RedundancyCom95
codon1	a std::string of length 3
codon2	a std::string of length 3
weights3	a weighting scheme for the pathways

Note: length of codons is checked by assert()

Definition at line 60 of file ThreeSubs.cc.

◆ P0()

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

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

Definition at line 232 of file ThreeSubs.cc.

◆ P2S()

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

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

Definition at line 237 of file ThreeSubs.cc.

◆ P2V()

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

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

Definition at line 242 of file ThreeSubs.cc.

◆ P4()

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

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

Definition at line 247 of file ThreeSubs.cc.

◆ Q0()

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

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

Definition at line 252 of file ThreeSubs.cc.

◆ Q2S()

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

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

Definition at line 257 of file ThreeSubs.cc.

◆ Q2V()

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

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

Definition at line 262 of file ThreeSubs.cc.

◆ Q4()

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

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

Definition at line 267 of file ThreeSubs.cc.

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

Public Member Functions