Module: Mapper::ConstantsInGenotype

Included in:
DepthLocusEmbConsts
Defined in:
../lib/mapper_constants.rb

Overview

See Mapper::DepthLocusEmbConsts for details.

Defined Under Namespace

Classes: EmbeddedConstantData

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Instance Attribute Details

- (Object) embedded (readonly)

Returns the value of attribute embedded 



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# File '../lib/mapper_constants.rb', line 23

def embedded
  @embedded
end

Instance Method Details

- (Object) embedded_constants=(config) 



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# File '../lib/mapper_constants.rb', line 25

def embedded_constants= config
  @embedded = {}
  config.each_pair do |name,params|
    raise "ConstantsInGenotype: missing min for constant '#{name}'" unless params.has_key? 'min'
    min = params['min']
    
    raise "ConstantsInGenotype: missing max for constant '#{name}'" unless params.has_key? 'max'       
    max = params['max']

    codons = params.has_key?('codons') ? params['codons'] : 1

    type = (min.integer? and max.integer?) ? Integer : Float
    size = 2 ** (@codon.bit_size * codons)
    step = (max - min).to_f / (size-1)
    @embedded[name] = EmbeddedConstantData.new( type, codons, min, step )
  end
end

- (Object) modify_expansion_base(exp, genome) 



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# File '../lib/mapper_constants.rb', line 43

def modify_expansion_base( exp, genome )
  return unless defined? @embedded
  exp.each do |token|
    next unless token.type == :literal 
    found = @embedded.fetch( token.data, nil )
    next if found.nil?

    index = 0
    found.codons.times do 
      index <<= @codon.bit_size

      position = @used_length.divmod( genome.size ).last         
      @used_length += 1

      index += @codon.raw_read genome.at(position)
    end

    token.data = found.mapping(index).to_s 
  end
end

- (Object) modify_expansion_generate(exp, genome) 



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# File '../lib/mapper_constants.rb', line 64

def modify_expansion_generate( exp, genome )
  return unless defined? @embedded
  exp.each do |token|
    next unless token.type == :literal 
    found = @embedded.fetch( token.data, nil )
    next if found.nil?

    index = 0
    found.codons.times do 
      index <<= @codon.bit_size
      value = @codon.rand_gen
      index += value
      genome.push value
    end

    token.data = found.mapping(index).to_s
  end
end