Class: Bio::BioAlignment::Codon

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-alignment/codonsequence.rb

Overview

Codon element for the matrix, used by CodonSequence.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(codon, codon_table = 1) ⇒ Codon

Returns a new instance of Codon.



11
12
13
14
 
# File 'lib/bio-alignment/codonsequence.rb', line 11

def initialize codon, codon_table = 1
  @codon = codon
  @codon_table = codon_table
end

Instance Attribute Details

#codon_table ⇒ Object (readonly)

Returns the value of attribute codon_table.



9
10
11
 
# File 'lib/bio-alignment/codonsequence.rb', line 9

def codon_table
  @codon_table
end

Instance Method Details

#gap? ⇒ Boolean

Returns:

  • (Boolean) 


16
17
18
 
# File 'lib/bio-alignment/codonsequence.rb', line 16

def gap?
  @codon == '---'
end

#to_aa ⇒ Object

lazily convert to Amino acid (once only)



33
34
35
36
37
38
39
40
41
42
43
44
45
 
# File 'lib/bio-alignment/codonsequence.rb', line 33

def to_aa
  aa = translate
  if not aa
    if gap?
      return '-'
    elsif undefined?
      return 'X'
    else
      raise 'What?'
    end
  end
  aa
end

#to_s ⇒ Object 



28
29
30
 
# File 'lib/bio-alignment/codonsequence.rb', line 28

def to_s
  @codon
end

#undefined? ⇒ Boolean

Returns:

  • (Boolean) 


20
21
22
23
24
25
26
 
# File 'lib/bio-alignment/codonsequence.rb', line 20

def undefined?
  aa = translate
  if aa == nil and not gap?
    return true
  end
  false
end