Calculate length statistics for divergence calculations. More...

#include <Sequence/Sites.hpp>

Public Member Functions
	Sites (const Sequence::Seq &seq1, const Sequence::Seq &seq2, const RedundancyCom95 &sitesObj, int maxdiffs=3)

	Sites (Sites &&)=default

void	operator() (const Sequence::Seq &seq1, const Sequence::Seq &seq2, const RedundancyCom95 &sitesObj, int maxdiffs=3)

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 58 of file Sites.hpp.

Member Function Documentation

◆ L0()

double Sequence::Sites::L0 ( void ) const

Returns: alignment length in terms of non-degenerate sites

Definition at line 133 of file Sites.cc.

◆ L2S()

double Sequence::Sites::L2S ( void ) const

Returns: alignment length in terms of transitional-degenerate sites

Definition at line 140 of file Sites.cc.

◆ L2V()

double Sequence::Sites::L2V ( void ) const

Returns: alignment length in terms of transversional-degenerate sites

Definition at line 147 of file Sites.cc.

◆ L4()

double Sequence::Sites::L4 ( void ) const

Returns: alignment length in terms of fourfold-degenerate sites

Definition at line 154 of file Sites.cc.