Refactors DNA Mutations; Refactors Mutations to use Traits (#15483)

* Refactors Mutations

* traits

* more work

* styling fix

* yet even more work

* oh hush

* almost there

* it continues yet further

* and that's genetics done

* and that's it folks

* last bit and golem fixup

* oof

* oops

* tweaks and fixes

* styling

code/modules/surgery/organs/augments_internal.dm

@@ -215,6 +215,14 @@
 	slot = "brain_clownvoice"
 	origin_tech = "materials=2;biotech=2"
 
+/obj/item/organ/internal/cyberimp/brain/clown_voice/insert(mob/living/carbon/M, special = FALSE)
+	..()
+	ADD_TRAIT(M, TRAIT_COMIC_SANS, "augment")
+
+/obj/item/organ/internal/cyberimp/brain/clown_voice/remove(mob/living/carbon/M, special = FALSE)
+	REMOVE_TRAIT(M, TRAIT_COMIC_SANS, "augment")
+	return ..()
+
 /obj/item/organ/internal/cyberimp/brain/speech_translator //actual translating done in human/handle_speech_problems
 	name = "Speech translator implant"
 	desc = "While known as a translator, this implant actually generates speech based on the user's thoughts when activated, completely bypassing the need to speak."

code/modules/surgery/organs/blood.dm

@@ -22,7 +22,7 @@
 		bleed_rate = 0
 		return
 
-	if(bodytemperature >= TCRYO && !(NOCLONE in mutations)) //cryosleep or husked people do not pump the blood.
+	if(bodytemperature >= TCRYO && !HAS_TRAIT(src, TRAIT_BADDNA)) //cryosleep or husked people do not pump the blood.
 		if(blood_volume < BLOOD_VOLUME_NORMAL)
 			blood_volume += 0.1 // regenerate blood VERY slowly
 
@@ -74,10 +74,10 @@
 
 		var/additional_bleed = round(clamp((reagents.get_reagent_amount("heparin") / 10), 0, 2), 1) //Heparin worsens existing bleeding
 
-		if(internal_bleeding_rate && !(status_flags & FAKEDEATH))
+		if(internal_bleeding_rate && !HAS_TRAIT(src, TRAIT_FAKEDEATH))
 			bleed_internal(internal_bleeding_rate + additional_bleed)
 
-		if(bleed_rate && !bleedsuppress && !(status_flags & FAKEDEATH))
+		if(bleed_rate && !bleedsuppress && !HAS_TRAIT(src, TRAIT_FAKEDEATH))
 			bleed(bleed_rate + additional_bleed)
 
 //Makes a blood drop, leaking amt units of blood from the mob
@@ -224,7 +224,7 @@
 /mob/living/carbon/human/get_blood_id()
 	if(dna.species.exotic_blood)//some races may bleed water..or kethcup..
 		return dna.species.exotic_blood
-	else if((NO_BLOOD in dna.species.species_traits) || (NOCLONE in mutations))
+	else if((NO_BLOOD in dna.species.species_traits) || HAS_TRAIT(src, TRAIT_HUSK))
 		return
 	return "blood"
 

code/modules/surgery/organs/body_egg.dm

@@ -12,19 +12,19 @@
 
 /obj/item/organ/internal/body_egg/insert(var/mob/living/carbon/M, special = 0)
 	..()
-	owner.status_flags |= XENO_HOST
+	ADD_TRAIT(owner, TRAIT_XENO_HOST, TRAIT_GENERIC)
+	ADD_TRAIT(owner, TRAIT_XENO_IMMUNE, "xeno immune")
 	START_PROCESSING(SSobj, src)
 	owner.med_hud_set_status()
-	spawn(0)
-		AddInfectionImages(owner)
+	INVOKE_ASYNC(src, .proc/AddInfectionImages, owner)
 
 /obj/item/organ/internal/body_egg/remove(var/mob/living/carbon/M, special = 0)
 	STOP_PROCESSING(SSobj, src)
 	if(owner)
-		owner.status_flags &= ~(XENO_HOST)
+		REMOVE_TRAIT(owner, TRAIT_XENO_HOST, TRAIT_GENERIC)
+		REMOVE_TRAIT(owner, TRAIT_XENO_IMMUNE, "xeno immune")
 		owner.med_hud_set_status()
-		spawn(0)
-			RemoveInfectionImages(owner)
+		INVOKE_ASYNC(src, .proc/RemoveInfectionImages, owner)
 	. = ..()
 
 /obj/item/organ/internal/body_egg/process()

code/modules/surgery/organs/ears.dm

@@ -13,39 +13,41 @@
 	// the person will not have either `deaf` or `ear_damage` decrease
 	// without external aid (earmuffs, drugs)
 	var/ear_damage = 0
+	// Multiplier for both long term and short term ear damage
+	var/damage_multiplier = 1
 
 /obj/item/organ/internal/ears/on_life()
 	if(!iscarbon(owner))
 		return
 	var/mob/living/carbon/C = owner
-	// genetic deafness prevents the body from using the ears, even if healthy
-	if(DEAF in C.mutations)
-		deaf = max(deaf, 1)
+	if(ear_damage < 100)
+		AdjustEarDamage(-0.1)
+
+	// if we have non-damage related deafness like mutations, quirks or clothing (earmuffs), don't bother processing here. Ear healing from earmuffs or chems happen elsewhere
+	if(HAS_TRAIT_NOT_FROM(C, TRAIT_DEAF, EAR_DAMAGE))
+		return
+
+	if(ear_damage >= 100)
+		deaf = max(deaf, 1) // if we're failing we always have at least 1 deaf stack (and thus deafness)
 	else
-		if(ishuman(C))
-			var/mob/living/carbon/human/H = C
-			if((H.l_ear && H.l_ear.flags_2 & HEALS_EARS_2) || (H.r_ear && H.r_ear.flags_2 & HEALS_EARS_2))
-				deaf = max(deaf - 1, 1)
-				ear_damage = max(ear_damage - 0.10, 0)
-		// if higher than UNHEALING_EAR_DAMAGE, no natural healing occurs.
-		if(ear_damage < UNHEALING_EAR_DAMAGE)
-			ear_damage = max(ear_damage - 0.05, 0)
-			deaf = max(deaf - 1, 0)
+		deaf = max(deaf - 1, 0)
+		if((ear_damage > 10) && prob(ear_damage / 30))
+			AdjustEarDamage(0, 4)
+			SEND_SOUND(owner, sound('sound/weapons/flash_ring.ogg'))
+
+	if(deaf)
+		ADD_TRAIT(owner, TRAIT_DEAF, EAR_DAMAGE)
+	else
+		REMOVE_TRAIT(owner, TRAIT_DEAF, EAR_DAMAGE)
+
 
 /obj/item/organ/internal/ears/proc/RestoreEars()
 	deaf = 0
 	ear_damage = 0
 
-	var/mob/living/carbon/C = owner
-	if(istype(C) && (DEAF in C.mutations))
-		deaf = 1
-
 /obj/item/organ/internal/ears/proc/AdjustEarDamage(ddmg, ddeaf)
-	ear_damage = max(ear_damage + ddmg, 0)
-	deaf = max(deaf + ddeaf, 0)
-
-/obj/item/organ/internal/ears/proc/MinimumDeafTicks(value)
-	deaf = max(deaf, value)
+	ear_damage = clamp(ear_damage + (ddmg * damage_multiplier), 0, 100)
+	deaf = max(deaf + (ddeaf * damage_multiplier), 0)
 
 /obj/item/organ/internal/ears/surgeryize()
 	RestoreEars()
@@ -61,20 +63,16 @@
 	if(ears)
 		ears.AdjustEarDamage(ddmg, ddeaf)
 
-/mob/living/carbon/MinimumDeafTicks(value)
-	var/obj/item/organ/internal/ears/ears = get_int_organ(/obj/item/organ/internal/ears)
-	if(ears)
-		ears.MinimumDeafTicks(value)
-
 /obj/item/organ/internal/ears/cybernetic
 	name = "cybernetic ears"
 	icon_state = "ears-c"
 	desc = "a basic cybernetic designed to mimic the operation of ears."
 	origin_tech = "biotech=4"
 	status = ORGAN_ROBOT
+	damage_multiplier = 0.9
 
 /obj/item/organ/internal/ears/cybernetic/emp_act(severity)
 	if(emp_proof)
 		return
 	..()
-	AdjustEarDamage(30, 120)
+	ear_damage += 40 / severity

code/modules/surgery/organs/eyes.dm

@@ -30,7 +30,7 @@
 	return eyes_icon
 
 /obj/item/organ/internal/eyes/proc/get_colourmatrix() //Returns a special colour matrix if the eyes are organic and the mob is colourblind, otherwise it uses the current one.
-	if(!is_robotic() && (COLOURBLIND in owner.mutations))
+	if(!is_robotic() && HAS_TRAIT(owner, TRAIT_COLORBLIND))
 		return colourblind_matrix
 	else
 		return colourmatrix
@@ -44,26 +44,26 @@
 	if(istype(M) && eye_colour)
 		M.update_body() //Apply our eye colour to the target.
 
-	if(!(COLOURBLIND in M.mutations) && (COLOURBLIND in dependent_disabilities)) //If the eyes are colourblind and we're not, carry over the gene.
-		dependent_disabilities -= COLOURBLIND
-		M.dna.SetSEState(GLOB.colourblindblock,1)
-		genemutcheck(M,GLOB.colourblindblock,null,MUTCHK_FORCED)
+	if(!HAS_TRAIT(M, TRAIT_COLORBLIND) && (TRAIT_COLORBLIND in dependent_disabilities)) //If the eyes are colourblind and we're not, carry over the gene.
+		dependent_disabilities -= TRAIT_COLORBLIND
+		M.dna.SetSEState(GLOB.colourblindblock, TRUE)
+		singlemutcheck(M, GLOB.colourblindblock, MUTCHK_FORCED)
 	else
 		M.update_client_colour() //If we're here, that means the mob acquired the colourblindness gene while they didn't have eyes. Better handle it.
 
 /obj/item/organ/internal/eyes/remove(mob/living/carbon/human/M, special = 0)
-	if(!special && (COLOURBLIND in M.mutations)) //If special is set, that means these eyes are getting deleted (i.e. during set_species())
-		if(!(COLOURBLIND in dependent_disabilities)) //We only want to change COLOURBLINDBLOCK and such it the eyes are being surgically removed.
-			dependent_disabilities |= COLOURBLIND
-		M.dna.SetSEState(GLOB.colourblindblock,0)
-		genemutcheck(M,GLOB.colourblindblock,null,MUTCHK_FORCED)
+	if(!special && HAS_TRAIT(M, TRAIT_COLORBLIND)) //If special is set, that means these eyes are getting deleted (i.e. during set_species())
+		if(!(TRAIT_COLORBLIND in dependent_disabilities)) //We only want to change COLOURBLINDBLOCK and such it the eyes are being surgically removed.
+			dependent_disabilities |= TRAIT_COLORBLIND
+		M.dna.SetSEState(GLOB.colourblindblock, FALSE)
+		singlemutcheck(M, GLOB.colourblindblock, MUTCHK_FORCED)
 	. = ..()
 
 /obj/item/organ/internal/eyes/surgeryize()
 	if(!owner)
 		return
-	owner.CureNearsighted()
-	owner.CureBlind()
+	owner.cure_nearsighted(EYE_DAMAGE)
+	owner.cure_blind(EYE_DAMAGE)
 	owner.SetEyeBlurry(0)
 	owner.SetEyeBlind(0)
 

code/modules/surgery/organs/lungs.dm

@@ -87,6 +87,9 @@
 	if((H.status_flags & GODMODE))
 		return
 
+	if(HAS_TRAIT(H, TRAIT_NOBREATH))
+		return
+
 	if(!breath || (breath.total_moles() == 0))
 		if(isspaceturf(loc))
 			H.adjustOxyLoss(10)
@@ -267,11 +270,7 @@
 /obj/item/organ/internal/lungs/proc/handle_breath_temperature(datum/gas_mixture/breath, mob/living/carbon/human/H) // called by human/life, handles temperatures
 	var/breath_temperature = breath.temperature
 
-	var/species_traits = list()
-	if(H && H.dna.species && H.dna.species.species_traits)
-		species_traits = H.dna.species.species_traits
-
-	if(!(COLDRES in H.mutations) && !(RESISTCOLD in species_traits)) // COLD DAMAGE
+	if(!HAS_TRAIT(H, TRAIT_RESISTCOLD)) // COLD DAMAGE
 		var/CM = abs(H.dna.species.coldmod)
 		var/TC = 0
 		if(breath_temperature < cold_level_3_threshold)
@@ -287,7 +286,7 @@
 			if(prob(20))
 				to_chat(H, "<span class='warning'>You feel [cold_message] in your [name]!</span>")
 
-	if(!(HEATRES in H.mutations) && !(RESISTHOT in species_traits)) // HEAT DAMAGE
+	if(!HAS_TRAIT(H, TRAIT_RESISTHEAT)) // HEAT DAMAGE
 		var/HM = abs(H.dna.species.heatmod)
 		var/TH = 0
 		if(breath_temperature > heat_level_1_threshold && breath_temperature < heat_level_2_threshold)

code/modules/surgery/organs/organ.dm

@@ -100,7 +100,7 @@
 		return
 
 	//Process infections
-	if(is_robotic() || sterile || (owner && (NO_GERMS in owner.dna.species.species_traits)))
+	if(is_robotic() || sterile || (owner && HAS_TRAIT(owner, TRAIT_NOGERMS)))
 		germ_level = 0
 		return
 

code/modules/surgery/organs/organ_external.dm

@@ -616,7 +616,7 @@ Note that amputating the affected organ does in fact remove the infection from t
 			"<span class='danger'>Something feels like it shattered in your [name]!</span>",\
 			"You hear a sickening crack.")
 		playsound(owner, "bonebreak", 150, 1)
-		if(owner.dna.species && !(NO_PAIN in owner.dna.species.species_traits))
+		if(!HAS_TRAIT(owner, TRAIT_NOPAIN))
 			owner.emote("scream")
 
 	status |= ORGAN_BROKEN

code/modules/surgery/organs/organ_internal.dm

@@ -239,25 +239,20 @@
 
 /obj/item/organ/internal/honktumor/insert(mob/living/carbon/M, special = 0)
 	..()
-	M.mutations.Add(CLUMSY)
-	M.mutations.Add(GLOB.comicblock)
-	M.dna.SetSEState(GLOB.clumsyblock,1,1)
-	M.dna.SetSEState(GLOB.comicblock,1,1)
-	genemutcheck(M,GLOB.clumsyblock,null,MUTCHK_FORCED)
-	genemutcheck(M,GLOB.comicblock,null,MUTCHK_FORCED)
+	M.dna.SetSEState(GLOB.clumsyblock, TRUE, TRUE)
+	M.dna.SetSEState(GLOB.comicblock, TRUE, TRUE)
+	singlemutcheck(M, GLOB.clumsyblock, MUTCHK_FORCED)
+	singlemutcheck(M, GLOB.comicblock, MUTCHK_FORCED)
 	organhonked = world.time
 	M.AddElement(/datum/element/waddling)
 	squeak = M.AddComponent(/datum/component/squeak, list('sound/items/bikehorn.ogg' = 1), 50)
 
 /obj/item/organ/internal/honktumor/remove(mob/living/carbon/M, special = 0)
 	. = ..()
-
-	M.mutations.Remove(CLUMSY)
-	M.mutations.Remove(GLOB.comicblock)
-	M.dna.SetSEState(GLOB.clumsyblock,0)
-	M.dna.SetSEState(GLOB.comicblock,0)
-	genemutcheck(M,GLOB.clumsyblock,null,MUTCHK_FORCED)
-	genemutcheck(M,GLOB.comicblock,null,MUTCHK_FORCED)
+	M.dna.SetSEState(GLOB.clumsyblock, FALSE)
+	M.dna.SetSEState(GLOB.comicblock, FALSE)
+	singlemutcheck(M, GLOB.clumsyblock, MUTCHK_FORCED)
+	singlemutcheck(M, GLOB.comicblock, MUTCHK_FORCED)
 	M.RemoveElement(/datum/element/waddling)
 	QDEL_NULL(squeak)
 	qdel(src)
@@ -268,7 +263,7 @@
 		to_chat(owner, "<font color='red' size='7'>HONK</font>")
 		owner.SetSleeping(0)
 		owner.Stuttering(20)
-		owner.MinimumDeafTicks(30)
+		owner.AdjustEarDamage(0, 30)
 		owner.Weaken(3)
 		owner << 'sound/items/airhorn.ogg'
 		if(prob(30))

code/modules/surgery/organs/pain.dm

@@ -34,7 +34,7 @@
 	if(stat >= UNCONSCIOUS)
 		return
 
-	if(NO_PAIN in dna.species.species_traits)
+	if(HAS_TRAIT(src, TRAIT_NOPAIN))
 		return
 	if(reagents.has_reagent("morphine"))
 		return
@@ -54,7 +54,7 @@
 
 	if(stat >= UNCONSCIOUS)
 		return
-	if(NO_PAIN in dna.species.species_traits)
+	if(HAS_TRAIT(src, TRAIT_NOPAIN))
 		return
 	if(reagents.has_reagent("morphine"))
 		return

code/modules/surgery/organs/subtypes/xenos.dm

@@ -125,11 +125,13 @@
 	M.faction |= "alien"
 	M.add_language("Hivemind")
 	M.add_language("Xenomorph")
+	ADD_TRAIT(M, TRAIT_XENO_IMMUNE, "xeno immune")
 
 /obj/item/organ/internal/xenos/hivenode/remove(mob/living/carbon/M, special = 0)
 	M.faction -= "alien"
 	M.remove_language("Hivemind")
 	M.remove_language("Xenomorph")
+	REMOVE_TRAIT(M, TRAIT_XENO_IMMUNE, "xeno immune")
 	. = ..()
 
 /obj/item/organ/internal/xenos/neurotoxin