class Bio::PAML::Codeml::PositiveSite

A record of codon sites, across the sequences in the alignment, showing evidence of positive selection.

This class is used for storing both codeml's full Bayesian and naive Bayesian analysis

Attributes

aaref[R]
omega[R]
p[R]
position[R]
probability[R]

Public Class Methods

new(fields) click to toggle source
# File lib/bio/appl/paml/codeml/report.rb, line 492
def initialize fields
  @position    = fields[0].to_i
  @aaref       = fields[1].to_s
  @probability = fields[2].to_f
  @omega       = fields[3].to_f
end

Public Instance Methods

dN_dS() click to toggle source

Return dN/dS (or omega) for this codon

# File lib/bio/appl/paml/codeml/report.rb, line 500
def dN_dS
  omega
end
Also aliased as: w
to_a() click to toggle source

Return contents as Array - useful for printing

# File lib/bio/appl/paml/codeml/report.rb, line 509
def to_a
  [ @position, @aaref, @probability, @omega ]
end
w()
Alias for: dN_dS