/obj/item/sequence_scanner
	name = "genetic sequence scanner"
	icon = 'icons/obj/devices/scanner.dmi'
	icon_state = "gene"
	inhand_icon_state = "healthanalyzer"
	worn_icon_state = "healthanalyzer"
	lefthand_file = 'icons/mob/inhands/equipment/medical_lefthand.dmi'
	righthand_file = 'icons/mob/inhands/equipment/medical_righthand.dmi'
	desc = "A hand-held scanner for analyzing someones gene sequence on the fly. Use on a DNA console to update the internal database."
	obj_flags = CONDUCTS_ELECTRICITY
	item_flags = NOBLUDGEON
	slot_flags = ITEM_SLOT_BELT
	throwforce = 3
	w_class = WEIGHT_CLASS_TINY
	throw_speed = 3
	throw_range = 7
	custom_materials = list(/datum/material/iron=SMALL_MATERIAL_AMOUNT*2)

	var/list/discovered = list() //hit a dna console to update the scanners database
	var/list/buffer
	var/ready = TRUE
	var/cooldown = (20 SECONDS)
	/// genetic makeup data that's scanned
	var/list/genetic_makeup_buffer = list()

/obj/item/sequence_scanner/examine(mob/user)
	. = ..()
	. += span_notice("Use primary attack to scan mutations, Secondary attack to scan genetic makeup")
	if(LAZYLEN(genetic_makeup_buffer) > 0)
		. += span_notice("It has the genetic makeup of \"[genetic_makeup_buffer["name"]]\" stored inside its buffer")

/obj/item/sequence_scanner/interact_with_atom(atom/interacting_with, mob/living/user, list/modifiers)
	if(istype(interacting_with, /obj/machinery/computer/scan_consolenew))
		var/obj/machinery/computer/scan_consolenew/console = interacting_with
		if(console.stored_research)
			to_chat(user, span_notice("[name] linked to central research database."))
			discovered = console.stored_research.discovered_mutations
		else
			to_chat(user,span_warning("No database to update from."))
		return ITEM_INTERACT_SUCCESS

	if(!isliving(interacting_with))
		return NONE

	add_fingerprint(user)

	//no scanning if its a husk or DNA-less Species
	if (!HAS_TRAIT(interacting_with, TRAIT_GENELESS) && !HAS_TRAIT(interacting_with, TRAIT_BADDNA))
		user.visible_message(span_notice("[user] analyzes [interacting_with]'s genetic sequence."))
		balloon_alert(user, "sequence analyzed")
		playsound(user, 'sound/items/healthanalyzer.ogg', 50) // close enough
		gene_scan(interacting_with, user)
		return ITEM_INTERACT_SUCCESS

	user.visible_message(span_notice("[user] fails to analyze [interacting_with]'s genetic sequence."), span_warning("[interacting_with] has no readable genetic sequence!"))
	return ITEM_INTERACT_BLOCKING

/obj/item/sequence_scanner/interact_with_atom_secondary(atom/interacting_with, mob/living/user, list/modifiers)
	if(istype(interacting_with, /obj/machinery/computer/scan_consolenew))
		var/obj/machinery/computer/scan_consolenew/console = interacting_with
		var/buffer_index = tgui_input_number(user, "Slot:", "Which slot to export:", 1, LAZYLEN(console.genetic_makeup_buffer), 1)
		console.genetic_makeup_buffer[buffer_index] = genetic_makeup_buffer
		return ITEM_INTERACT_SUCCESS

	if(!isliving(interacting_with))
		return NONE

	add_fingerprint(user)

	//no scanning if its a husk, DNA-less Species or DNA that isn't able to be copied by a changeling/disease
	if (!HAS_TRAIT(interacting_with, TRAIT_GENELESS) && !HAS_TRAIT(interacting_with, TRAIT_BADDNA) && !HAS_TRAIT(interacting_with, TRAIT_NO_DNA_COPY))
		user.visible_message(span_warning("[user] is scanning [interacting_with]'s genetic makeup."))
		if(!do_after(user, 3 SECONDS, interacting_with))
			balloon_alert(user, "scan failed!")
			user.visible_message(span_warning("[user] fails to scan [interacting_with]'s genetic makeup."))
			return ITEM_INTERACT_BLOCKING
		makeup_scan(interacting_with, user)
		balloon_alert(user, "makeup scanned")
		return ITEM_INTERACT_SUCCESS

	user.visible_message(span_notice("[user] fails to analyze [interacting_with]'s genetic makeup."), span_warning("[interacting_with] has no readable genetic makeup!"))
	return ITEM_INTERACT_BLOCKING

/obj/item/sequence_scanner/attack_self(mob/user)
	display_sequence(user)

/obj/item/sequence_scanner/attack_self_tk(mob/user)
	return

///proc for scanning someone's mutations
/obj/item/sequence_scanner/proc/gene_scan(mob/living/carbon/target, mob/living/user)
	if(!iscarbon(target) || !target.has_dna())
		return

	//add target mutations to list as well as extra mutations.
	//dupe list as scanner could modify target data
	buffer = LAZYLISTDUPLICATE(target.dna.mutation_index)
	var/list/active_mutations = list()
	for(var/datum/mutation/human/mutation in target.dna.mutations)
		LAZYSET(buffer, mutation.type, GET_SEQUENCE(mutation.type))
		active_mutations.Add(mutation.type)

	to_chat(user, span_notice("Subject [target.name]'s DNA sequence has been saved to buffer."))
	for(var/mutation in buffer)
		//highlight activated mutations
		if(LAZYFIND(active_mutations, mutation))
			to_chat(user, span_boldnotice("[get_display_name(mutation)]"))
		else
			to_chat(user, span_notice("[get_display_name(mutation)]"))

///proc for scanning someone's genetic makeup
/obj/item/sequence_scanner/proc/makeup_scan(mob/living/carbon/target, mob/living/user)
	if(!iscarbon(target) || !target.has_dna())
		return

	genetic_makeup_buffer = list(
	"label"="Analyzer Slot:[target.real_name]",
	"UI"=target.dna.unique_identity,
	"UE"=target.dna.unique_enzymes,
	"UF"=target.dna.unique_features,
	"name"=target.real_name,
	"blood_type"=target.dna.blood_type)

/obj/item/sequence_scanner/proc/display_sequence(mob/living/user)
	if(!LAZYLEN(buffer) || !ready)
		return
	var/list/options = list()
	for(var/mutation in buffer)
		options += get_display_name(mutation)

	var/answer = tgui_input_list(user, "Analyze Potential", "Sequence Analyzer", sort_list(options))
	if(isnull(answer))
		return
	if(!ready || !user.can_perform_action(src, NEED_LITERACY|NEED_LIGHT|FORBID_TELEKINESIS_REACH))
		return

	var/sequence
	for(var/mutation in buffer) //this physically hurts but i dont know what anything else short of an assoc list
		if(get_display_name(mutation) == answer)
			sequence = buffer[mutation]
			break

	if(sequence)
		var/display
		for(var/i in 0 to length_char(sequence) / DNA_MUTATION_BLOCKS-1)
			if(i)
				display += "-"
			display += copytext_char(sequence, 1 + i*DNA_MUTATION_BLOCKS, DNA_MUTATION_BLOCKS*(1+i) + 1)

		to_chat(user, "[span_boldnotice("[display]")]<br>")

	ready = FALSE
	icon_state = "[icon_state]_recharging"
	addtimer(CALLBACK(src, PROC_REF(recharge)), cooldown, TIMER_UNIQUE)

/obj/item/sequence_scanner/proc/recharge()
	icon_state = initial(icon_state)
	ready = TRUE

/obj/item/sequence_scanner/proc/get_display_name(mutation)
	var/datum/mutation/human/human_mutation = GET_INITIALIZED_MUTATION(mutation)
	if(!human_mutation)
		return "ERROR"
	if(mutation in discovered)
		return  "[human_mutation.name] ([human_mutation.alias])"
	else
		return human_mutation.alias