#define BAD_INIT_QDEL_BEFORE 1
#define BAD_INIT_DIDNT_INIT 2
#define BAD_INIT_SLEPT 4
#define BAD_INIT_NO_HINT 8

SUBSYSTEM_DEF(atoms)
	name = "Atoms"
	init_order = INIT_ORDER_ATOMS
	flags = SS_NO_FIRE

	var/old_initialized

	var/list/late_loaders = list()

	var/list/BadInitializeCalls = list()

	initialized = INITIALIZATION_INSSATOMS

/datum/controller/subsystem/atoms/Initialize(timeofday)
	GLOB.fire_overlay.appearance_flags = RESET_COLOR
	setupGenetics() //to set the mutations' sequence

	initialized = INITIALIZATION_INNEW_MAPLOAD
	InitializeAtoms()
	initialized = INITIALIZATION_INNEW_REGULAR
	return ..()

/datum/controller/subsystem/atoms/proc/InitializeAtoms(list/atoms)
	if(initialized == INITIALIZATION_INSSATOMS)
		return

	old_initialized = initialized
	initialized = INITIALIZATION_INNEW_MAPLOAD

	var/count
	var/list/mapload_arg = list(TRUE)

	if(atoms)
		count = atoms.len
		for(var/I in 1 to count)
			var/atom/A = atoms[I]
			if(!(A.flags_1 & INITIALIZED_1))
				InitAtom(A, mapload_arg)
				CHECK_TICK
	else
		count = 0
		for(var/atom/A in world)
			if(!(A.flags_1 & INITIALIZED_1))
				InitAtom(A, mapload_arg)
				++count
				CHECK_TICK

	testing("Initialized [count] atoms")
	pass(count)

	initialized = old_initialized

	if(late_loaders.len)
		for(var/I in 1 to late_loaders.len)
			var/atom/A = late_loaders[I]
			A.LateInitialize()
		testing("Late initialized [late_loaders.len] atoms")
		late_loaders.Cut()

/// Init this specific atom
/datum/controller/subsystem/atoms/proc/InitAtom(atom/A, list/arguments)
	var/the_type = A.type
	if(QDELING(A))
		BadInitializeCalls[the_type] |= BAD_INIT_QDEL_BEFORE
		return TRUE

	var/start_tick = world.time

	var/result = A.Initialize(arglist(arguments))

	if(start_tick != world.time)
		BadInitializeCalls[the_type] |= BAD_INIT_SLEPT

	var/qdeleted = FALSE

	if(result != INITIALIZE_HINT_NORMAL)
		switch(result)
			if(INITIALIZE_HINT_LATELOAD)
				if(arguments[1])	//mapload
					late_loaders += A
				else
					A.LateInitialize()
			if(INITIALIZE_HINT_QDEL)
				qdel(A)
				qdeleted = TRUE
			else
				BadInitializeCalls[the_type] |= BAD_INIT_NO_HINT

	if(!A)	//possible harddel
		qdeleted = TRUE
	else if(!(A.flags_1 & INITIALIZED_1))
		BadInitializeCalls[the_type] |= BAD_INIT_DIDNT_INIT
	else
		SEND_SIGNAL(A,COMSIG_ATOM_AFTER_SUCCESSFUL_INITIALIZE)

	return qdeleted || QDELING(A)

/datum/controller/subsystem/atoms/proc/map_loader_begin()
	old_initialized = initialized
	initialized = INITIALIZATION_INSSATOMS

/datum/controller/subsystem/atoms/proc/map_loader_stop()
	initialized = old_initialized

/datum/controller/subsystem/atoms/Recover()
	initialized = SSatoms.initialized
	if(initialized == INITIALIZATION_INNEW_MAPLOAD)
		InitializeAtoms()
	old_initialized = SSatoms.old_initialized
	BadInitializeCalls = SSatoms.BadInitializeCalls

/datum/controller/subsystem/atoms/proc/setupGenetics()
	var/list/mutations = subtypesof(/datum/mutation/human)
	shuffle_inplace(mutations)
	for(var/A in subtypesof(/datum/generecipe))
		var/datum/generecipe/GR = A
		GLOB.mutation_recipes[initial(GR.required)] = initial(GR.result)
	for(var/i in 1 to LAZYLEN(mutations))
		var/path = mutations[i] //byond gets pissy when we do it in one line
		var/datum/mutation/human/B = new path ()
		B.alias = "Mutation [i]"
		GLOB.all_mutations[B.type] = B
		GLOB.full_sequences[B.type] = generate_gene_sequence(B.blocks)
		GLOB.alias_mutations[B.alias] = B.type
		if(B.locked)
			continue
		if(B.quality == POSITIVE)
			GLOB.good_mutations |= B
		else if(B.quality == NEGATIVE)
			GLOB.bad_mutations |= B
		else if(B.quality == MINOR_NEGATIVE)
			GLOB.not_good_mutations |= B
		CHECK_TICK

/datum/controller/subsystem/atoms/proc/InitLog()
	. = ""
	for(var/path in BadInitializeCalls)
		. += "Path : [path] \n"
		var/fails = BadInitializeCalls[path]
		if(fails & BAD_INIT_DIDNT_INIT)
			. += "- Didn't call atom/Initialize()\n"
		if(fails & BAD_INIT_NO_HINT)
			. += "- Didn't return an Initialize hint\n"
		if(fails & BAD_INIT_QDEL_BEFORE)
			. += "- Qdel'd in New()\n"
		if(fails & BAD_INIT_SLEPT)
			. += "- Slept during Initialize()\n"

/datum/controller/subsystem/atoms/Shutdown()
	var/initlog = InitLog()
	if(initlog)
		text2file(initlog, "[GLOB.log_directory]/initialize.log")