--function forestry_bees.Bee(bee_type,active_type_gene,inactive_type_gene,active_fertility_gene,inactive_fertility_gene)
    --local itemstack = ItemStack({name = forestry_bees.bee_name(bee_type,active_type_gene)})
    --itemstack:get_meta():set_string("active_type_gene",active_type_gene)
    --itemstack:get_meta():set_string("inactive_type_gene",inactive_type_gene)
    --itemstack:get_meta():set_string("active_fertility_gene",active_fertility_gene)
    --itemstack:get_meta():set_string("inactive_fertility_gene",inactive_fertility_gene)
    --return itemstack
--end

function forestry_bees.Bee(bee_type,genes)
    local itemstack = ItemStack({name = forestry_bees.bee_name(bee_type,genes["type_gene"][1])})  --the "1" is cuz the table genes["type_gene"] has 2 entries: active and inactive
    itemstack:get_meta():set_string("genes", minetest.serialize(genes))
    --for gene_type,gene in pairs(genes) do
    --    itemstack:get_meta():set_string(gene_type,gene)
    --end
    return itemstack
end

function forestry_bees.can_queen_work(queen, pos)
	local genes = minetest.deserialize(queen:get_meta():get_string("genes"))
	local biome_data = minetest.get_biome_data(pos)
	local biome_name = minetest.get_biome_name(biome_data["biome"])
	local humidity = biome_data["humidity"]
	local heat = biome_data["heat"]
	--now get the environmental data
	local is_right_heat = true --futureproofing
	local is_right_humidity = true --futureproofing
	local is_right_biome = true --futureproofing
	local is_sky_access = (genes["cave"][1] or (minetest.get_natural_light(vector.offset(pos, 0, 1, 0), 0.5) == 15))
	local is_not_raining = (genes["flyer"][1] or true) --would require additional mods
	local is_day =  (genes["nocturnal"][1] or ((0.25 < minetest.get_timeofday()) and (minetest.get_timeofday() < 0.75)))
	return is_sky_access and is_not_raining and is_day
end

function forestry_bees.calculate_drop(bee)
    local genes = minetest.deserialize(bee:get_meta():get_string("genes"))
    local possible_drops = forestry_bees.bee_drops[genes["type_gene"][1]] --this gets us a table
    local out_table = {}
    for drop,chance in pairs(possible_drops) do
        if math.random() < chance * genes["production"][1] then   --the prob of getting something is P = (base chance from bee_drops) * (item modifier (frames and stuff)) * (bee production gene)
            table.insert(out_table,ItemStack(drop))
        end
    end
    return out_table
end

function forestry_bees.bee_name(bee_type,active_type_gene)
    return "forestry_bees:"..active_type_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.format_bee(bee)
  local name = bee:get_name()
  local meta = bee:get_meta()
  local genes = forestry_bees.return_all_genes_double(string.sub(string.match(string.match(name,":.*"),".*_"),2,-2))
  return forestry_bees.Bee(string.sub(string.match(string.sub(string.match(name,"_.*"),2),"_.*"),2),genes)
end

function forestry_bees.breed_princess_drone(princess,drone)
  local princess_genes = minetest.deserialize(princess:get_meta():get_string("genes")) --princess_meta["genes"]
  local drone_genes = minetest.deserialize(drone:get_meta():get_string("genes"))
  --fix for missing genes in bees, if we have bees with missing genes we just give them the default ones
  if princess_genes == nil then
      local princess_type = string.sub(string.match(string.match(princess:get_name(),":.*"),".*_"),2,-2)
      princess_genes = forestry_bees.return_all_genes_double(princess_type)
  end
  if drone_genes == nil then
      local drone_type = string.sub(string.match(string.match(drone:get_name(),":.*"),".*_"),2,-2)
      drone_genes = forestry_bees.return_all_genes_double(drone_type)
  end
	local queen = forestry_bees.Bee("queen",princess_genes)
  local queen_meta = queen:get_meta()
  queen_meta:set_string("drone_genes",minetest.serialize(drone_genes))
  return queen
end

local function final_gene(gene1,gene2)
  local output = {}
	--randomly choose if the genes are 1,2 or 2,1
	if math.random(2)==2 then
		output[1] = gene1
		output[2] = gene2
	else
		output[1] = gene2
		output[2] = gene1	
	end
  return output
end

local function mutation(type1,type2,pos)
	local out_table1 = {}
	local out_table2 = {}
  local mutation = {false, false}
	--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, t in pairs(forestry_bees.bee_mutations[type1][type2]) do
			local prob1 = math.random()
			local prob2 = math.random()
      local flag = t["check_fun"](pos)
			if (t["chance"] > prob1) and flag then
				table.insert(out_table1, out_type)
			end
			if (t["chance"] > prob2) and flag then
				table.insert(out_table2, out_type)
			end
		end	
	end

	local output = final_gene(type1,type2)

	if next(out_table1) then --if a mutation accurred in gene 1
    mutation[1] = true
		output[1] = out_table1[math.random(#out_table1)]
	end
	if next(out_table2) then --if a mutation accurred in gene 2
    mutation[2] = true
		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, mutation
end

local function choose_genes(genes)
    --from the table "genes" we for each entry randomly choose 1,2 and keep that gene
    --returning a table
    local output = {}
    for key,gene_pair in pairs(genes) do
        output[key] = gene_pair[math.random(2)]
    end
    return output
end

local function output_genes(mother_genes,father_genes,pos)
	local mother_chosen_genes = choose_genes(mother_genes)
	local father_chosen_genes = choose_genes(father_genes)
  local genes = {}
  
  genes["type_gene"], is_mutated = mutation(mother_chosen_genes["type_gene"], father_chosen_genes["type_gene"],pos)
  
  for key,_ in pairs(mother_chosen_genes) do
    --if key == "type_gene" then
    --  genes[key] = mutation(mother_chosen_genes[key], father_chosen_genes[key])
    if not (key == "type_gene") then
      genes[key] = final_gene(mother_chosen_genes[key], father_chosen_genes[key])
    end
  end
  --if a mutation occurred we change the corresponding genes to the base_genes of the mutated bee
  if is_mutated[1] then
      for key,value in pairs(forestry_bees.return_genes(genes["type_gene"][1])) do
          genes[key][1] = value
      end
  end
  if is_mutated[2] then
      for key,value in pairs(forestry_bees.return_genes(genes["type_gene"][2])) do
          genes[key][2] = value
      end
  end
  return genes
end

function forestry_bees.apiary_result(queen, pos)
	--given a queen calculates the correct princess + drone output
	local meta = queen:get_meta()
	local mother_genes = minetest.deserialize(meta:get_string("genes"))         
	local father_genes = minetest.deserialize(meta:get_string("drone_genes"))   
	local genes = output_genes(mother_genes,father_genes,pos)
	--local genes = final_gene(mother_chosen_gene, father_chosen_gene)
	local princess = forestry_bees.Bee("princess", genes)
	local dronelist = {}
  local fertility = mother_genes["fertility"][1]
	for i=1,fertility do 
		local genes = output_genes(mother_genes,father_genes,pos)
		local drone = forestry_bees.Bee("drone", genes)
		table.insert(dronelist, drone)
	end
	return princess, dronelist
end