Class: Mapper::CodonMod

Inherits:

Object

• Object
• Mapper::CodonMod

show all

Defined in:

../lib/codon_mod.rb

Overview

Instance Attribute Summary (collapse)

• - (Object) bit_size

  The number of bits per codon.

• - (Object) random

  The source of randomness, used for calling “random.rand( limit )”, defaulting to ‘Kernel’ class.

Instance Method Summary (collapse)

• - (Object) generate(numof_choices, index, dummy = nil)

  Create the codon from the index of the choice and a number of choices.

• - (CodonMod) initialize(bit_size = 8) constructor

  Initialise a codon representation.

• - (Object) interpret(numof_choices, codon, dummy = nil)

  Interpret the codon given a number of choices, returning the index:.

• - (Object) mutate_bit(codon)

  Mutate a single bit in the source codon, return the mutated codon.

• - (Object) rand_gen

  Generate a valid random codon.

• - (Object) raw_read(codon)

  Read a raw codon value.

• - (Boolean) valid_codon?(codon)

  Return true if the codon is valid.

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# File '../lib/codon_mod.rb', line 10

def initialize( bit_size=8 )
  self.bit_size= bit_size
  @random = Kernel
end

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# File '../lib/codon_mod.rb', line 19

def bit_size
  @bit_size
end

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# File '../lib/codon_mod.rb', line 16

def random
  @random
end

  codon = index unmod numof_choices 

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# File '../lib/codon_mod.rb', line 47

def generate( numof_choices, index, dummy=nil )
  raise "CodonMod: cannot accomodate #{numof_choices} choices in #{@bit_size}-bit codon" if numof_choices > @card
  raise "CodonMod: index (#{index}) must be lower than numof choices (#{numof_choices})" if index >= numof_choices
  return index if numof_choices == 0
  index + numof_choices * @random.rand( @card/numof_choices )
end

  index = codon mod numof_choices

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# File '../lib/codon_mod.rb', line 31

def interpret( numof_choices, codon, dummy=nil )
  raise "CodonMod: codon #{codon} out of range 0..#{@card-1}" unless valid_codon? codon
  codon.divmod(numof_choices).last
end

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# File '../lib/codon_mod.rb', line 65

def mutate_bit codon
  codon ^ (2 ** @random.rand( @bit_size ))
end

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# File '../lib/codon_mod.rb', line 55

def rand_gen
  @random.rand @card
end

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# File '../lib/codon_mod.rb', line 60

def raw_read codon
  codon
end

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# File '../lib/codon_mod.rb', line 70

def valid_codon? codon
  codon >= 0 and codon < @card
end