genetica 0.0.1.beta.1

data/lib/genetica.rb

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+require 'genetica/chromosome'
+require 'genetica/chromosome_builder'
+require 'genetica/population'
+require 'genetica/population_builder'

data/lib/genetica/chromosome.rb

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+module Genetica
+  class Chromosome
+
+    attr_reader :chromosome
+
+    def initialize(chromosome)
+      @chromosome = chromosome
+    end
+
+    def single_point_crossover(chromosome)
+      other_chromosome = chromosome.chromosome
+      locus = rand(other_chromosome.size) + 1
+
+      offspring_a = @chromosome.take(locus) + other_chromosome.last(@chromosome.size - locus)
+      offspring_b = other_chromosome.take(locus) + @chromosome.last(@chromosome.size - locus)
+
+      return Chromosome.new(offspring_a), Chromosome.new(offspring_b)
+    end
+
+    def mutate!(mutation_probability, alleles)
+      if mutation_probability > 0
+        @chromosome.collect! do |gene|
+          if rand.between? 0, mutation_probability
+            # Mutated Gene, we select a different gene from the alleles
+            (alleles - [gene]).sample
+          else
+            # Gene without mutation
+            gene
+          end
+        end
+      end
+    end
+
+    def to_s
+      return @chromosome.join
+    end
+
+  end
+end
+

data/lib/genetica/chromosome_builder.rb

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+module Genetica
+  class ChromosomeBuilder
+
+    attr_accessor :length
+    attr_accessor :alleles
+
+    def initialize
+      # Default Chromosome values
+      @length = 8
+      @alleles = [0, 1]
+    end
+    
+    def chromosome
+      chromosome = Array.new
+      @length.times { chromosome << @alleles.sample }
+      return Chromosome.new(chromosome)
+    end
+
+  end
+end

data/lib/genetica/population.rb

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+module Genetica
+  class Population
+
+    attr_reader :population
+    attr_reader :generation
+
+    attr_accessor :alleles
+    attr_accessor :crossover_probability
+    attr_accessor :mutation_probability
+    attr_accessor :fitness_function
+
+    def initialize(population)
+      @generation = 0
+      @population = population
+    end
+
+    def best_chromosome
+      @population.at @population_fitness.index(self.best_fitness)
+    end
+
+    def best_fitness
+      @population_fitness.max
+    end
+
+    def average_fitness
+      @population_fitness.inject(:+) / @population_fitness.size.to_f
+    end
+
+    def population_fitness
+      @population.collect { |chromosome| @fitness_function.call(chromosome) }
+    end
+
+    def fitness_function=(new_fitness_function)
+      @fitness_function = new_fitness_function
+      @population_fitness = self.population_fitness
+    end
+
+    def population=(new_population)
+      @population = new_population
+      @population_fitness = self.population_fitness
+    end
+
+    def fitness_proportionate_selection
+      # FUTURE: With Ruby 1.9.3 you can use rand with ranges, e.g. rand 0.0..3.4
+      # Get random number
+      random_generator = Random.new
+      random_number = random_generator.rand 0.0..@population_fitness.inject(:+)
+
+      # Chromosome selection
+      fitness_counter = 0
+      @population.each_with_index do |chromosome, i|
+        fitness_counter += @population_fitness[i]
+        if fitness_counter >= random_number
+          return chromosome
+        end
+      end
+    end
+
+    def run(generations=1)
+      generations.times do
+        # Generate a new chromosome population
+        population = Array.new
+
+        while population.size < @population.size
+          # 1. Selection Step
+          # Select a pair of parent chromosomes from the current population.
+          # This selection is 'with replacement', the same chromosome can be selected
+          # more than once to become a parent.
+          chromosome_a = self.fitness_proportionate_selection
+          chromosome_b = self.fitness_proportionate_selection
+
+          # 2. Crossover Step
+          # TODO: Maybe crossover probability check would be in the single_point_crossover of
+          # Chromosome class.
+          if @crossover_probability > 0 and rand.between? 0, @crossover_probability
+            offspring_a, offspring_b = chromosome_a.single_point_crossover chromosome_b
+          else
+            offspring_a, offspring_b = chromosome_a, chromosome_b
+          end
+
+          # 3. Mutation Step
+          offspring_a.mutate! @mutation_probability, @alleles
+          offspring_b.mutate! @mutation_probability, @alleles
+
+          # 4. Adding offsprings to new chromosome population
+          population << offspring_a << offspring_b          
+        end
+
+        # If original population size is odd discard a random chromosome
+        population.delete_at rand population.size if @population.size.odd?
+
+        # Replacing chromosome population with the new one
+        self.population = population
+
+        # A new generation has been created
+        @generation += 1
+      end
+    end
+
+  end
+end

data/lib/genetica/population_builder.rb

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+module Genetica
+  class PopulationBuilder
+
+    # Population attributes
+    attr_accessor :size
+    attr_accessor :crossover_probability
+    attr_accessor :mutation_probability
+    attr_accessor :fitness_function
+    # Chromosome attributes
+    attr_accessor :chromosome_length
+    attr_accessor :chromosome_alleles
+
+    def initialize
+      # Default Population values
+      @size = 20
+      @crossover_probability = 0.7
+      @mutation_probability = 0.001
+      @fitness_function = nil
+      # Default Chromosome values
+      @chromosome_length = 8
+      @chromosome_alleles = [0, 1]
+    end
+
+    def population
+      # Generating Chromosome population
+      chromosome_builder = ChromosomeBuilder.new
+      chromosome_builder.length = @chromosome_length
+      chromosome_builder.alleles = @chromosome_alleles
+
+      chromosome_population = Array.new
+      @size.times { chromosome_population << chromosome_builder.chromosome }
+
+      # Generating Population 
+      population = Population.new chromosome_population
+      population.alleles = @chromosome_alleles
+      population.crossover_probability = @crossover_probability
+      population.mutation_probability = @mutation_probability
+      population.fitness_function = @fitness_function
+      
+      return population
+    end
+
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: genetica
+version: !ruby/object:Gem::Version
+  version: 0.0.1.beta.1
+  prerelease: 6
+platform: ruby
+authors:
+- José Francisco Calvo
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-09-08 00:00:00.000000000 +02:00
+default_executable: 
+dependencies: []
+description: Genetica is a library to create and use Genetic Algorithms solutions
+  using Ruby language.
+email: josefranciscocalvo@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/genetica.rb
+- lib/genetica/chromosome.rb
+- lib/genetica/chromosome_builder.rb
+- lib/genetica/population.rb
+- lib/genetica/population_builder.rb
+has_rdoc: true
+homepage: http://dev.monsterzen.com/projects/genetica.html
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.6.2
+signing_key: 
+specification_version: 3
+summary: The Ruby Genetic Algorithms Gem.
+test_files: []