Module: Genotype::Cohort

Extended by:
Entity, Workflow
Defined in:
lib/rbbt/entity/genotype.rb

Constant Summary

Constants included from Entity

Entity::UNPERSISTED_PREFIX

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.extended(cohort) ⇒ Object 



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# File 'lib/rbbt/entity/genotype.rb', line 31

def self.extended(cohort)
  prev_genotype_cohort_extended(cohort) if self.respond_to? :prev_genotype_cohort_extended

  cohort.each do |genotype| genotype.extend Genotype unless Genotype === genotype end

  cohort.helper :metagenotype do
    cohort.metagenotype
  end

  cohort.helper :samples do
    cohort
  end

  NamedArray.setup(cohort, cohort.collect{|genotype| genotype.jobname})
end

.prev_genotype_cohort_extended ⇒ Object 



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# File 'lib/rbbt/entity/genotype.rb', line 27

alias prev_genotype_cohort_extended extended

Instance Method Details

#jobname ⇒ Object 



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# File 'lib/rbbt/entity/genotype.rb', line 52

def jobname
  if @jobname.nil?
    if self.length > 3
      @jobname ||= "Meta-genotype: " + self.collect{|g| g.jobname}[0..2] * ", " + " + #{self.length - 3} more"
    else
      @jobname ||= "Meta-genotype: " + self.collect{|g| g.jobname} * ", "
    end
    @jobname[100..-1] = " (etc. #{self.length} genotypes)" if @jobname.length > 135
  end
  @jobname
end

#metagenotype ⇒ Object 



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# File 'lib/rbbt/entity/genotype.rb', line 64

def metagenotype
  organism = self.collect{|g| g.organism}.compact.first
  orig_watson = self.collect{|g| g.watson}.compact.first
  GenomicMutation.setup(self.dup.flatten, jobname, organism, orig_watson).extend Genotype
end

#subset(genotypes) ⇒ Object 



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# File 'lib/rbbt/entity/genotype.rb', line 47

def subset(genotypes)
  new = self.values_at *(genotypes & fields)
  new.extend Cohort
end