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
492 def initialize fields
493   @position    = fields[0].to_i
494   @aaref       = fields[1].to_s
495   @probability = fields[2].to_f
496   @omega       = fields[3].to_f
497 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
500 def dN_dS
501   omega
502 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
509 def to_a
510   [ @position, @aaref, @probability, @omega ]
511 end
w()
Alias for: dN_dS