Method SampleOffspring

avida-core/source/analyze/cAnalyze.cc:1604–1691

JEB: Creates specified number of offspring by running each organism in the test CPU with mutations on.

// JEB: Creates specified number of offspring by running
// each organism in the test CPU with mutations on.
void cAnalyze::SampleOffspring(cString cur_string)
{
  int number_to_sample = (cur_string.GetSize()) ? cur_string.PopWord().AsInt() : 1000;
  
  // These parameters copied from BatchRecalculate, they could change what kinds of offspring are produced!!
  Apto::Array<int> manual_inputs;  // Used only if manual inputs are specified
  cString msg;                // Holds any information we may want to send the driver to display
  int use_resources      = (cur_string.GetSize()) ? cur_string.PopWord().AsInt() : 0;
  int update             = (cur_string.GetSize()) ? cur_string.PopWord().AsInt() : -1;
  bool use_random_inputs = (cur_string.GetSize()) ? cur_string.PopWord().AsInt() == 1: false;
  bool use_manual_inputs = false;
  
  //Manual inputs will override random input request and must be the last arguments.
  if (cur_string.CountNumWords() > 0){
    if (cur_string.CountNumWords() == m_world->GetEnvironment().GetInputSize()){
      manual_inputs.Resize(m_world->GetEnvironment().GetInputSize());
      use_random_inputs = false;
      use_manual_inputs = true;
      for (int k = 0; cur_string.GetSize(); k++)
        manual_inputs[k] = cur_string.PopWord().AsInt();
    } else if (m_world->GetVerbosity() >= VERBOSE_ON) {
      cerr << "warning: Invalid number of environment inputs requested for recalculation: " << cur_string.CountNumWords()
           << " specified, " << m_world->GetEnvironment().GetInputSize() << " required." << endl;
    }
  }
  
  cCPUTestInfo test_info(1); //we only allow one generation of testing! v. important to get proper offspring
  if (use_manual_inputs)
    test_info.UseManualInputs(manual_inputs);
  else
    test_info.UseRandomInputs(use_random_inputs); 
  test_info.SetResourceOptions(use_resources, m_resources, update, m_resource_time_spent_offset);

  if (m_world->GetVerbosity() >= VERBOSE_ON) {
    msg.Set("Sampling %d offspring from each of the %d organisms in batch %d...", number_to_sample, batch[cur_batch].GetSize(), cur_batch);
    cout << msg << endl;
  } else{ 
    msg.Set("Sampling offspring...");
    cout << msg << endl;
  }
  
  // Load the mutation rates from the environment.
  test_info.MutationRates().Copy(m_world->GetEnvironment().GetMutRates());
  // Copy them into the organism  
  tListPlus<cAnalyzeGenotype> offspring_list;
  tListIterator<cAnalyzeGenotype> batch_it(batch[cur_batch].List());
  cAnalyzeGenotype* parent_genotype = NULL;

  cTestCPU * test_cpu = m_world->GetHardwareManager().CreateTestCPU(m_ctx);  
  while ((parent_genotype = batch_it.Next())) {
    
    // We keep a hash with genome strings as keys
    // to save duplication of the same offspring genotype.
    // NumCPUs is incremented whenever an offspring is
    // created more than once from the same parent.
    Apto::Map<Apto::String, cAnalyzeGenotype*> genome_hash;
    
    for (int i=0; i<number_to_sample; i++) {