population random_breeder::breed(const population &generation, const std::vector<double> &fitnesses) const
{
  using namespace std;  
  
  population ret;
  tree_crossover_reproducer repr;
  node_crossover_reproducer mrepr;
  builder random_builder;
  experimental_parameters e = exp_params();
  const uint32_t growth_tree_min = e["growth_tree_min"];
  const uint32_t growth_tree_max = e["growth_tree_max"];
  while(ret.size() < generation.size())
  {
    const agent &mother = generation[rand() % generation.size()];
    const agent &father = generation[rand() % generation.size()];
    agent mutant      = random_builder.grow(program_types_set, growth_tree_min, growth_tree_max);
    const vector<agent> children = repr.reproduce(vector<agent> { mother, father });
    if(children.size() > 0)
    {
      agent res0        = mrepr.reproduce(vector<agent> { children[0], mutant })[0];
      ret.push_back(res0);
    }
    if(children.size() > 1)
    {
      agent res1        = mrepr.reproduce(vector<agent> { children[1], mutant })[0];
      ret.push_back(res1);
    }
  }
  return ret;
}

void report(population& p)
{
  switch(cfg.report_every)
  {
    case config::report::none:
      break;
    case config::report::avg:
      {
        float avg = 0.0;
        for(auto i = p.begin(); i != p.end(); ++i)
          avg += i->eval;
        avg /= static_cast<float>(p.size());
        std::cout << iter << ' ' << avg << '\n';
      }
      break;
    case config::report::best:
      std::cout << iter << ' ' << p[0].eval << '\n';
      break;
  }
  
  if(cfg.report_var)
  {
    std::cout << iter << ' ' << statistics::variance(p) << '\n';
  }
}

 void increase_tree_depth(generation_table& gtable, population& pop, int& from_depth, combo::arity_t& needed_arg_count, int fill_from_arg, const reduct::rule& reduction_rule) {
     for (population::iterator it = pop.begin(); it != pop.end(); ++it) {
         int number_of_combinations = 1;
         bool can_have_leaves = false;
         std::vector<generation_table::iterator> assignment;
         std::vector<combo::combo_tree::leaf_iterator> leaves;
         for (combo::combo_tree::leaf_iterator lit = it->begin_leaf(); lit != it->end_leaf(); ++lit) {
             if (combo::is_argument(*lit))
                 if (combo::get_argument(*lit).abs_idx() <= needed_arg_count)
                     continue;
             for (std::vector<generation_node>::iterator it2 = gtable.begin(); it2 != gtable.end(); it2++)
                 if (combo::equal_type_tree(it2->node, combo::infer_vertex_type(*it, lit))) {
                     if (it2->glist.size() != 0)
                         can_have_leaves = true;
                     assignment.push_back(it2);
                     number_of_combinations *= it2->glist.size();                        
                     break;
                 }
         }
         if (!can_have_leaves)
             number_of_combinations = 0;
         for (int i = 0; i < number_of_combinations; i++) {
             combo::combo_tree temp_tree(*it);
             int ongoing_count = 1;
             leaves.clear();
             for (combo::combo_tree::leaf_iterator lit = temp_tree.begin_leaf(); lit != temp_tree.end_leaf(); ++lit)
                 leaves.push_back(lit);
             std::vector<generation_table::iterator>::iterator it2 = assignment.begin();
             for (std::vector<combo::combo_tree::leaf_iterator>::iterator lit = leaves.begin(); lit != leaves.end(); ++lit) {
                 if (combo::is_argument(**lit))
                     if (combo::get_argument(**lit).abs_idx() <= needed_arg_count)
                        continue;
                 if ((*it2)->glist.size() != 0) {
                     node_list::iterator it3 = (*it2)->glist.begin();
                     for (int n = 0; n < (int)(i/(number_of_combinations/(ongoing_count * (*it2)->glist.size())) % (*it2)->glist.size()); n++)
                         it3++;
                     temp_tree.replace(*lit, *it3);
                     ongoing_count *= (*it2)->glist.size();
                 }
                 it2++;
             }
             bool erased = true;
             for (combo::combo_tree::leaf_iterator lit = temp_tree.begin_leaf(); lit != temp_tree.end_leaf(); ++lit) {
                 if (combo::get_arity(*lit) != 0 && !combo::is_argument(*lit)) {
                     erased = false;
                     break;
                 }
             }
             if (combo::does_contain_all_arg_up_to(temp_tree, needed_arg_count)) {
                 erased = false;
             }
             if (!erased) {
                 //Uses less memory but is very slow
                 /*fill_leaves_single(temp_tree, fill_from_arg);
                 reduced_insertion(new_pop, temp_tree, reduction_rule);*/
                 pop.push_front(temp_tree);
             }
         }
     }
 }

family_vector rnd_selector::select(const population&p,const int fcount)
{
  family_vector result(fcount);
  for(int i=0;i<fcount;i++)
    result[i]=std::make_pair(m_random.uniform(0,p.size()-1),
			     m_random.uniform(0,p.size()-1));
  return result;
}

void adapt_population(population& p)
{
  float F_min = min_element(p.begin(),p.end(),eval_comp)->eval;
  for(unsigned int i=0; i<p.size(); i++)
  {
    float sum = 0.0;
    for(unsigned int j=0; j<p.size(); j++)
      sum += p[j].eval - F_min;
    p[i].adapt = (p[i].eval - F_min)/sum;
  }
}

std::vector<population::individual_type> best_s_policy::select(const population &pop) const
{
	const population::size_type migration_rate = get_n_individuals(pop);
	// Create a temporary array of individuals.
	std::vector<population::individual_type> result(pop.begin(),pop.end());
	// Sort the individuals (best go first).
	std::sort(result.begin(),result.end(),dom_comp(pop));
	// Leave only desired number of elements in the result.
	result.erase(result.begin() + migration_rate,result.end());
	return result;
}

 void fill_leaves(population& pop, int& from_arg) {
     for (population::iterator it = pop.begin(); it != pop.end(); ++it) {
         int local_from_arg = from_arg;
         for (combo::combo_tree::leaf_iterator lit = it->begin_leaf(); lit != it->end_leaf(); ++lit) {
             if (!combo::is_argument(*lit)) {
                 combo::arity_t number_of_leaves = combo::get_arity(*lit);
                 if (number_of_leaves < 0) number_of_leaves = -1 * number_of_leaves + 1;
                 for (combo::arity_t count = 0; count < number_of_leaves; count++) {
                     (*it).append_child(lit, combo::argument(++local_from_arg));
                 }
             }
         }
     }
 }

void ms::evolve(population &pop) const
{
	// Let's store some useful variables.
	const population::size_type NP = pop.size();

	// Get out if there is nothing to do.
	if (m_starts == 0 || NP == 0) {
		return;
	}

	// Local population used in the algorithm iterations.
	population working_pop(pop);

	//ms main loop
	for (int i=0; i< m_starts; ++i)
	{
		working_pop.reinit();
		m_algorithm->evolve(working_pop);
		if (working_pop.problem().compare_fc(working_pop.get_individual(working_pop.get_best_idx()).cur_f,working_pop.get_individual(working_pop.get_best_idx()).cur_c,
			pop.get_individual(pop.get_worst_idx()).cur_f,pop.get_individual(pop.get_worst_idx()).cur_c
		) )
		{
			//update best population replacing its worst individual with the good one just produced.
			pop.set_x(pop.get_worst_idx(),working_pop.get_individual(working_pop.get_best_idx()).cur_x);
			pop.set_v(pop.get_worst_idx(),working_pop.get_individual(working_pop.get_best_idx()).cur_v);
		}
		if (m_screen_output)
		{
			std::cout << i << ". " << "\tCurrent iteration best: " << working_pop.get_individual(working_pop.get_best_idx()).cur_f << "\tOverall champion: " << pop.champion().f << std::endl;
		}
	}
}

void mutation_function(population& p)
{
  for(auto i = p.begin(); i != p.end(); ++i)
  {
    float prob = 1 - i->adapt; // probability of mutation
    float r = uniform_random(); // random float between <0,1)

    if(r < prob)
    {
      mutation::random_transposition(i->perm);
      i->eval = evaluation(i->perm); // after mutation is done we have to evaluate this specimen again
    }
  }
}

void replacement(population& p)
{
  std::sort(p.begin(), p.end(), eval_cmp());
  p.resize(population_size);
  
  if( p[0].eval < best_specimen.eval )
  {
    best_specimen = p[0];
    deviate_count = 0;
  }
  else
  {
    deviate_count++;
  }
}

void allocate_pop(population &pop,size_t NumDims,int stra_num,int num_obj)
{
	size_t pop_size=pop.size();
	size_t i;
	for ( i=0;i<pop_size;i++ )
		allocate_ind(pop[i],NumDims,stra_num,num_obj);
}

void reallocate_stra(population &pop,int stra_idx,int size,double val)
{
	int pop_size=pop.size();
	int i;
	for ( i=0;i<pop_size;i++ )
		pop[i].stra[stra_idx].assign(size,val);
}

std::vector<std::pair<population::size_type,std::vector<population::individual_type>::size_type> >
	random_r_policy::select(const std::vector<population::individual_type> &immigrants, const population &dest) const
{
	const population::size_type rate_limit = std::min<population::size_type>(get_n_individuals(dest),boost::numeric_cast<population::size_type>(immigrants.size()));
	// Temporary vectors to store sorted indices of the populations.
	std::vector<population::size_type> immigrants_idx(boost::numeric_cast<std::vector<population::size_type>::size_type>(immigrants.size()));
	std::vector<population::size_type> dest_idx(boost::numeric_cast<std::vector<population::size_type>::size_type>(dest.size()));
	// Fill in the arrays of indices.
	iota(immigrants_idx.begin(),immigrants_idx.end(),population::size_type(0));
	iota(dest_idx.begin(),dest_idx.end(),population::size_type(0));
	// Permute the indices (immigrants).
	for (population::size_type i = 0; i < rate_limit; ++i) {
		population::size_type next_idx = i + (m_urng() % (rate_limit - i));
		if (next_idx != i) {
			std::swap(immigrants_idx[i], immigrants_idx[next_idx]);
		}
	}
	// Permute the indices (destination).
	for (population::size_type i = 0; i < rate_limit; ++i) {
		population::size_type next_idx = i + (m_urng() % (dest.size() - i));
		if (next_idx != i) {
			std::swap(dest_idx[i], dest_idx[next_idx]);
		}
	}
	// Return value.
	std::vector<std::pair<population::size_type,std::vector<population::individual_type>::size_type> >
		retval;
	for (population::size_type i = 0; i < rate_limit; ++i) {
		retval.push_back(std::make_pair(dest_idx[i],immigrants_idx[i]));
	}
	return retval;
}

/**
 * @param[in] pop input population.
 *
 * @return the number of individuals to be migrated from/to the population according to the current migration rate and type.
 */
population::size_type base::get_n_individuals(const population &pop) const
{
	population::size_type retval = 0;
	switch (m_type) {
		case absolute:
			retval = boost::numeric_cast<population::size_type>(m_rate);
			if (retval > pop.size()) {
				pagmo_throw(value_error,"absolute migration rate is higher than population size");
			}
			break;
		case fractional:
			retval = boost::numeric_cast<population::size_type>(double_to_int::convert(m_rate * pop.size()));
			pagmo_assert(retval <= pop.size());
	}
	return retval;
}

void report_end(population& p)
{
  if(cfg.report_every == config::report::none)
  {
    if(cfg.report_population)
    {
      if(cfg.debug)
      {
        std::cout << "Reporting population\n";
        std::cout << "Evaluation = [ permutation ]\n";
      }
      std::sort(p.begin(), p.end(), eval_cmp());
      for(auto i = p.begin(); i != p.end(); ++i)
        std::cout << i->eval << " = " << i->perm << std::endl;
    }

    if(cfg.report_best)
    {
      if(cfg.debug)
      {
        std::cout << "Reporting best speciman\n";
        std::cout << "Evaluation = [ permutation ]\n";
      }
      std::cout << best_specimen.eval << " = " << best_specimen.perm << std::endl;
    }

    if(cfg.optimum > -1)
    {
      if(cfg.debug)
      {
        std::cout << "Reporting number of iterations needed to compute best specimen with given optimum value or --max-iter if optimum is not reached\n";
      }
      std::cout << iter << "\n";
    }

    if(cfg.compare_operators)
    {
      std::cout << "ox = " << ox_count << "\n";
      std::cout << "cx = " << cx_count << "\n";
      std::cout << "pmx = " << pmx_count << "\n";
      std::cout << "crossovers = " << x_count << "\n";
    }
  }
}

void init_prev_population()
{
  for(int i = 0; i < population_size; ++i)
  {
    specimen s;
    s.perm = permutation(N);
    s.eval = s.adapt = 0.0;
    prev_population.push_back(s);
  }
}

std::vector<population::individual_type> best_kill_s_policy::select(population &pop) const
{
	pagmo_assert(get_n_individuals(pop) <= pop.size());
	// Gets the number of individuals to select
	const population::size_type migration_rate = get_n_individuals(pop);
	// Create a temporary array of individuals.
	std::vector<population::individual_type> result;
	// Gets the indexes of the best individuals
	std::vector<population::size_type> best_idx = pop.get_best_idx(migration_rate);
	// Puts the best individuals in results
	for (population::size_type i =0; i< migration_rate; ++i) {
		result.push_back(pop.get_individual(best_idx[i]));
	}
	// Remove them from the original population 
	// (note: the champion will still carry information on the best guy ...)
	for (population::size_type i=0 ; i<migration_rate; ++i) {
		pop.reinit(best_idx[i]);
	}
	return result;
}

/// Evolve method.
void monte_carlo::evolve(population &pop) const
{
	// Let's store some useful variables.
	const problem::base &prob = pop.problem();
	const problem::base::size_type prob_dimension = prob.get_dimension(), prob_i_dimension = prob.get_i_dimension();
	const decision_vector &lb = prob.get_lb(), &ub = prob.get_ub();
	const population::size_type pop_size = pop.size();
	// Get out if there is nothing to do.
	if (pop_size == 0 || m_max_eval == 0) {
		return;
	}
	// Initialise temporary decision vector, fitness vector and decision vector.
	decision_vector tmp_x(prob_dimension);
	fitness_vector tmp_f(prob.get_f_dimension());
	constraint_vector tmp_c(prob.get_c_dimension());
	// Main loop.
	for (std::size_t i = 0; i < m_max_eval; ++i) {
		// Generate a random decision vector.
		for (problem::base::size_type j = 0; j < prob_dimension - prob_i_dimension; ++j) {
			tmp_x[j] = boost::uniform_real<double>(lb[j],ub[j])(m_drng);
		}
		for (problem::base::size_type j = prob_dimension - prob_i_dimension; j < prob_dimension; ++j) {
			tmp_x[j] = boost::uniform_int<int>(lb[j],ub[j])(m_urng);
		}
		// Compute fitness and constraints.
		prob.objfun(tmp_f,tmp_x);
		prob.compute_constraints(tmp_c,tmp_x);
		// Locate the worst individual.
		const population::size_type worst_idx = pop.get_worst_idx();
		if (prob.compare_fc(tmp_f,tmp_c,pop.get_individual(worst_idx).cur_f,pop.get_individual(worst_idx).cur_c)) {
			pop.set_x(worst_idx,tmp_x);
		}
	}
}

		// perform (\lambda+\mu) -> (\lambda) selection
		void dgea_alg::select(population& pop, population& child_pop)
		{
			int pop_size=pop.size();
			int num_dims=m_ppara->get_dim();
			int i;
			population pop_merged(pop_size);
			vector<vector<double> > prev_x(pop_size);
			for ( i=0;i<pop_size;i++ )
			{
				prev_x[i].resize(num_dims);
				pop_merged[i]=pop[i];
				// record previous x
				prev_x[i]=pop[i].x;
			}// for every individual

			// push child population at the tail of merged population
			copy( child_pop.begin(),child_pop.end(),back_inserter(pop_merged) );

			nth_element(pop_merged.begin(), pop_merged.begin()+pop_size, pop_merged.end());
			//// heap sorting
			//make_heap(pop_merged.begin(),pop_merged.end());
			//for ( i=0;i<pop_size;i++ )
			//{
			//	// record delta x for stat purpose
			//	pop_heap(pop_merged.begin(),pop_merged.end());
			//	pop_merged.pop_back();
			//	const individual& new_ind=pop_merged.front();
			//	pop[i]=new_ind;
			//	m_alg_stat.delta_x[i]=pop[i].x-prev_x[i];// pop_merged:{parents,offsprings}
			//}

			for ( i=0;i<pop_size;i++ )
			{
				pop[i]=pop_merged[i];
				// record delta x
				m_alg_stat.delta_x[i] = (pop[i].x-prev_x[i]);
			}// for every individual
		}// end function select

/**
 * Updates the constraints scaling vector with the given population.
 * @param[in] population pop.
 */
void cstrs_self_adaptive::update_c_scaling(const population &pop)
{
	if(*m_original_problem != pop.problem()) {
		pagmo_throw(value_error,"The problem linked to the population is not the same as the problem given in argument.");
	}

	// Let's store some useful variables.
	const population::size_type pop_size = pop.size();

	// get the constraints dimension
	//constraint_vector c(m_original_problem->get_c_dimension(), 0.);
	problem::base::c_size_type prob_c_dimension = m_original_problem->get_c_dimension();
	problem::base::c_size_type number_of_eq_constraints =
			m_original_problem->get_c_dimension() -
			m_original_problem->get_ic_dimension();

	const std::vector<double> &c_tol = m_original_problem->get_c_tol();

	m_c_scaling.resize(m_original_problem->get_c_dimension());
	std::fill(m_c_scaling.begin(),m_c_scaling.end(),0.);

	// evaluates the scaling factor
	for(population::size_type i=0; i<pop_size; i++) {
		// updates the current constraint vector
		const population::individual_type &current_individual = pop.get_individual(i);

		const constraint_vector &c = current_individual.cur_c;

		// computes scaling with the right definition of the constraints (can be in base problem? currently used
		// by con2mo as well)
		for(problem::base::c_size_type j=0; j<number_of_eq_constraints; j++) {
			m_c_scaling[j] = std::max(m_c_scaling[j], std::max(0., (std::abs(c.at(j)) - c_tol.at(j))) );
		}
		for(problem::base::c_size_type j=number_of_eq_constraints; j<prob_c_dimension; j++) {
			m_c_scaling[j] = std::max(m_c_scaling[j], std::max(0., c.at(j) - c_tol.at(j)) );
		}
	}
}