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

Calculate length statistics for divergence calculations. More...

#include <Sequence/Sites.hpp>

List of all members.

Public Member Functions
	Sites (const RedundancyCom95 *sitesObj, const Sequence::Seq *seq1, const Sequence::Seq *seq2, const int max=3, const int code=0)
double	L0 (void) const
double	L2S (void) const
double	L2V (void) const
double	L4 (void) const

---

Detailed Description

Calculate length statistics for divergence calculations.

This class calculates the length of each sequence in a pairwise comparison in terms of site degeneracy. The 4 values computed are:
1.) L0 -- the number of non-degenerate sites in the comparison.
2.) L2S -- the number of two-fold degenerate sites in the comparison for which transitions are synonymous.
3.) L2V -- the number of two-fold degenerate sites in the comparison for which transversion are synonymous.
4.) L4 -- the number of fourfold degenerate sites in the comparison.

In order to count these numbers, one has to know how degenerate each codon is, which is why objects of this type must be constructed with objects of type Sequence::RedundancyCom95.

Author:

Kevin Thornton

Definition at line 59 of file Sites.hpp.

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Constructor & Destructor Documentation

Sequence::Sites::Sites	(	const RedundancyCom95 *	sitesObj,
		const Sequence::Seq *	seq1,
		const Sequence::Seq *	seq2,
		const int	max = 3,
		const int	code = 0
	)			[explicit]

Parameters:

	sitesObj	an initialized object of type Sequence::RedundancyCom95
	seq1	a Sequence::Seq
	seq2	a Sequence::Seq
	max	max number of substitutions per codon to analyze
	code	see Sequence::GeneticCodes for valid values

Note:

sequences must be of same length, this is checked by assert()

sequence lengths must be multiples of 3, this is checked by assert()

Definition at line 40 of file Sites.cc.

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Member Function Documentation

double Sequence::Sites::L0

(

void

)

const [inline]

Returns:

alignment length in terms of non-degenerate sites

Definition at line 80 of file Sites.hpp.

double Sequence::Sites::L2S

(

void

)

const [inline]

Returns:

alignment length in terms of transitional-degenerate sites

Definition at line 87 of file Sites.hpp.

double Sequence::Sites::L2V

(

void

)

const [inline]

Returns:

alignment length in terms of transversional-degenerate sites

Definition at line 94 of file Sites.hpp.

double Sequence::Sites::L4

(

void

)

const [inline]

Returns:

alignment length in terms of fourfold-degenerate sites

Definition at line 101 of file Sites.hpp.

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

• Sites.hpp
• Sites.cc