function forestry_bees.Bee(bee_type,active_gene,inactive_gene)
    local itemstack = ItemStack({name = forestry_bees.bee_name(bee_type,active_gene)})
    itemstack:get_meta():set_string("active_gene",active_gene)
    itemstack:get_meta():set_string("inactive_gene",inactive_gene)
    return itemstack
end

function forestry_bees.bee_name(bee_type,active_gene)
    return "forestry_bees:"..active_gene.."_"..bee_type
end

function forestry_bees.stacks_in_inv(inv,listname)
  local stack_list = inv:get_list(listname)
  local result = 0
  for i = 1,#stack_list do
    if not stack_list[i]:is_empty() then
      result = result + 1
    end
  end
  return result
end

function forestry_bees.breed_princess_drone(princess,drone)
  local princess_meta = princess:get_meta()
  local drone_meta = drone:get_meta()
	local queen = forestry_bees.Bee("queen",
                                  princess_meta:get_string("active_gene"),
                                  princess_meta:get_string("inactive_gene"))
  local queen_meta = queen:get_meta()
  queen_meta:set_string("drone_active_gene",drone_meta:get_string("active_gene"))
  queen_meta:set_string("drone_inactive_gene",drone_meta:get_string("inactive_gene"))
  return queen
end

local function final_gene(type1,type2)
	local out_table1 = {}
	local out_table2 = {}
	--check every possible mutation to see if we may obtain it
	if ( (not (forestry_bees.bee_mutations[type1] == nil)) and (not (forestry_bees.bee_mutations[type1][type2] == nil)) ) then
		for out_type, chance in pairs(forestry_bees.bee_mutations[type1][type2]) do
			local prob1 = math.random()
			local prob2 = math.random()
			if chance > prob1 then
				table.insert(out_table1, out_type)
			end
			if chance > prob2 then
				table.insert(out_table2, out_type)
			end
		end	
	end
	--if we got no mutations then the eligible out_types are the input_types
	output = {}
	--randomly choose if the genes are 1,2 or 2,1
	if math.random(2)==2 then
		output[1] = type1
		output[2] = type2
	else
		output[1] = type2
		output[2] = type1	
	end
	if next(out_table1) then --if a mutation accurred in gene 1
		output[1] = out_table1[math.random(#out_table1)]
	end
	if next(out_table2) then --if a mutation accurred in gene 2
		output[2] = out_table2[math.random(#out_table2)]
	end
	--out_table is always non-empty, now we uniformally 
	--sample from out_table to get the output gene
	return output
end

function forestry_bees.apiary_result(queen)
	--given a queen calculates the correct princess + drone output
	local meta = queen:get_meta()
	local mother_genes = {meta:get_string("active_gene"),meta:get_string("inactive_gene")}
	local father_genes = {meta:get_string("drone_active_gene"),meta:get_string("drone_inactive_gene")}
	local mother_chosen_gene = mother_genes[math.random(#mother_genes)]
	local father_chosen_gene = father_genes[math.random(#father_genes)]
	local genes = final_gene(mother_chosen_gene, father_chosen_gene)
	local princess = forestry_bees.Bee("princess", genes[1], genes[2])
	local dronelist = {}
	for i=1,4 do --in future bees will have fertility and this number should change, so a little bit of futureproofing
		mother_chosen_gene = mother_genes[math.random(#mother_genes)]
		father_chosen_gene = father_genes[math.random(#father_genes)]
		local genes = final_gene(mother_chosen_gene, father_chosen_gene)
		local drone = forestry_bees.Bee("drone", genes[1], genes[2])
		table.insert(dronelist, drone)
	end
	return princess, dronelist
end