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

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

#include <Sequence/ThreeSubs.hpp>

List of all members.

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 51 of file ThreeSubs.hpp.

---

Constructor & Destructor Documentation

Sequence::ThreeSubs::~ThreeSubs

(

void

)

does nothing

Definition at line 36 of file ThreeSubs.cc.

---

Member Function Documentation

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
	code	see Sequence::GeneticCodes for valid values
	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 43 of file ThreeSubs.cc.

double Sequence::ThreeSubs::P0

(

void

)

const [inline]

Returns:

number of transitions at non-degenerate sites in the codon

Definition at line 68 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::P2S

(

void

)

const [inline]

Returns:

number of transitions at transitional-degenerate sites in the codon

Definition at line 77 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::P2V

(

void

)

const [inline]

Returns:

number of transitions at transversional-degenerate sites in the codon

Definition at line 86 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::P4

(

void

)

const [inline]

Returns:

number of transitions at fourfold-degenerate sites in the codon

Definition at line 95 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::Q0

(

void

)

const [inline]

Returns:

number of transversions at non-degenerate sites in the codon

Definition at line 104 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::Q2S

(

void

)

const [inline]

Returns:

number of transversions at transitional-degenerate sites in the codon

Definition at line 113 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::Q2V

(

void

)

const [inline]

Returns:

number of transversions at transversional-degenerate sites in the codon

Definition at line 122 of file ThreeSubs.hpp.

double Sequence::ThreeSubs::Q4

(

void

)

const [inline]

Returns:

number of transversions at fourfold-degenerate sites in the codon

Definition at line 131 of file ThreeSubs.hpp.

---

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

• ThreeSubs.hpp
• ThreeSubs.cc