Class: Bio::PAML::Codeml::PositiveSite

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/paml/codeml/report.rb

Overview

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fields) ⇒ PositiveSite

Returns a new instance of PositiveSite.



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# 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

Instance Attribute Details

#aaref ⇒ Object (readonly)

Returns the value of attribute aaref.



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# File 'lib/bio/appl/paml/codeml/report.rb', line 488

def aaref
  @aaref
end

#omega ⇒ Object (readonly)

Returns the value of attribute omega.



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# File 'lib/bio/appl/paml/codeml/report.rb', line 490

def omega
  @omega
end

#position ⇒ Object (readonly)

Returns the value of attribute position.



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# File 'lib/bio/appl/paml/codeml/report.rb', line 487

def position
  @position
end

#probability ⇒ Object (readonly) Also known as: p

Returns the value of attribute probability.



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# File 'lib/bio/appl/paml/codeml/report.rb', line 489

def probability
  @probability
end

Instance Method Details

#dN_dS ⇒ Object Also known as: w

Return dN/dS (or omega) for this codon



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# File 'lib/bio/appl/paml/codeml/report.rb', line 500

def dN_dS
  omega
end

#to_a ⇒ Object

Return contents as Array - useful for printing



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# File 'lib/bio/appl/paml/codeml/report.rb', line 509

def to_a
  [ @position, @aaref, @probability, @omega ]
end