Method PointMutate

avida-core/source/cpu/cHardwareBase.cc:1087–1164

}

int cHardwareBase::PointMutate(cAvidaContext& ctx, double override_mut_rate)
{
  const int max_genome_size = m_world->GetConfig().MAX_GENOME_SIZE.Get();
  const int min_genome_size = m_world->GetConfig().MIN_GENOME_SIZE.Get();
  
  cCPUMemory& memory = GetMemory();
  int totalMutations = 0;
  
//  const int num_muts = ctx.GetRandom().GetRandBinomial(memory.GetSize(), mut_rate);
//  
//  for (int i = 0; i < num_muts; i++) {
//    const int pos = ctx.GetRandom().GetUInt(memory.GetSize());
//    memory[pos] = m_inst_set->GetRandomInst(ctx);
//    memory.SetFlagMutated(pos);
//    memory.SetFlagPointMut(pos);
//  }

  
  // Point Substitution Mutations (per site)
  if (m_organism->GetPointMutProb() > 0.0 || override_mut_rate > 0.0) {
    double mut_rate = (override_mut_rate > 0.0) ? override_mut_rate : m_organism->GetPointMutProb();
    int num_mut = ctx.GetRandom().GetRandBinomial(memory.GetSize(), mut_rate);
    
    // If we have lines to mutate...
    if (num_mut > 0) {
      for (int i = 0; i < num_mut; i++) {
        int site = ctx.GetRandom().GetUInt(memory.GetSize());
        memory[site] = m_inst_set->GetRandomInst(ctx);
        totalMutations++;
      }
    }
  }
  
  // Point Insert Mutations (per site)
  if (m_organism->GetPointInsProb() > 0.0) {
    int num_mut = ctx.GetRandom().GetRandBinomial(memory.GetSize(), m_organism->GetPointInsProb());
    
    // If would make creature too big, insert up to max_genome_size
    if (num_mut + memory.GetSize() > max_genome_size) {
      num_mut = max_genome_size - memory.GetSize();
    }
    
    // If we have lines to insert...
    if (num_mut > 0) {
      // Build a sorted list of the sites where mutations occured
      Apto::Array<int> mut_sites(num_mut);
      for (int i = 0; i < num_mut; i++) mut_sites[i] = ctx.GetRandom().GetUInt(memory.GetSize() + 1);
      Apto::QSort(mut_sites);
      
      // Actually do the mutations (in reverse sort order)
      for (int i = mut_sites.GetSize() - 1; i >= 0; i--) {
        memory.Insert(mut_sites[i], m_inst_set->GetRandomInst(ctx));
      }
      
      totalMutations += num_mut;
    }
  }