/obj/machinery/centrifuge
name = "Centrifuge"
icon = 'icons/obj/pathology.dmi'
icon_state = "centrifuge0"
desc = "A large machine that can be used to separate a pathogen sample from a blood sample."
anchored = 1
density = 1
var/obj/item/bloodslide/source = null
var/datum/pathogen/isolated = null
var/obj/item/reagent_containers/glass/petridish/target = null
var/obj/item/reagent_containers/glass/beaker/beaker = null
var/on = 0
var/datum/pathogen/process_pathogen
var/obj/item/bloodslide/process_source
var/counter = 15
attack_hand(mob/user as mob)
var/output_text = "Centrifuge
"
if (src.on)
output_text = "The centrifuge is currently working. Emergency shutdown"
else
if (src.source)
output_text += "The centrifuge currently contains a [src.source]. Eject
"
else
output_text += "The centrifuge's source slot is empty.
"
if (src.source)
if (istype(src.source, /obj/item/bloodslide))
if (!src.source.reagents.has_reagent("blood"))
output_text += "The [src.source] contains no viable sample.
"
else
var/datum/reagent/blood/B = src.source.reagents.reagent_list["blood"]
if (B.volume && B.pathogens.len)
if (B.pathogens.len > 1)
output_text += "The centrifuge is calibrated to isolate a sample of [src.isolated ? src.isolated.name : "all pathogens"].
"
output_text += "The blood in the [src.source] contains multiple pathogens. Calibrate to isolate a sample of: "
output_text += "All "
for (var/uid in B.pathogens)
var/datum/pathogen/P = B.pathogens[uid]
output_text += "[P.name] "
output_text += " "
else
var/uid = B.pathogens[1]
var/datum/pathogen/P = B.pathogens[uid]
output_text += "The centrifuge will isolate the single sample of [P].
"
else
output_text += "The [src.source] contains no viable sample.
"
// TODO: not only blood slides can be used
else
output_text += "There is no isolation source inserted into the centrifuge.
"
if (src.target)
output_text += "There is a petri dish inserted into the machine. Eject
"
else
output_text += "There is no petri dish inserted into the machine.
"
output_text += "Begin isolation process"
/*if (src.target)
output_text += "The petri dish already contains a pathogen sample.
"
else
output_text += "The petri dish is empty and is ready to receive a pathogen sample.
"
*/
user << browse("Centrifuge[output_text]", "window=centrifuge")
onclose(user, "centrifuge")
return
Topic(href, href_list)
if (..())
return
if (href_list["ejectsrc"])
if (src.source && !src.on)
src.source.master = null
src.source.loc = src.loc
src.contents -= src.target
src.source.layer = initial(src.source.layer)
src.source = null
src.isolated = null
else if (href_list["ejectdish"])
if (src.target && !src.on)
src.target.master = null
src.target.loc = src.loc
src.contents -= src.target
src.target.layer = initial(src.target.layer)
src.target = null
else if (href_list["shutdown"])
if (src.on && alert("Are you sure you want to shut down the process?",,"Yes","No") == "Yes")
src.on = 0
src.icon_state = "centrifuge0"
src.visible_message("The centrifuge grinds to a sudden halt. The blood slide flies off the supports and shatters somewhere inside the machine.", "You hear a grinding noise, followed by something shattering.")
qdel(src.source)
src.source = null
src.isolated = null
counter = 15
processing_items.Remove(src)
else if (href_list["isolate"])
if (!src.on)
if (href_list["isolate"] == "All")
src.isolated = null
else
src.isolated = locate(href_list["isolate"])
else if (href_list["begin"])
var/maybegin = 1
if (!src.on)
if (!src.source)
boutput(usr, "You cannot begin isolation without a source container.")
maybegin = 0
else if (!src.source.reagents.has_reagent("blood"))
boutput(usr, "You cannot begin isolation without a source blood sample.")
maybegin = 0
else
var/datum/reagent/blood/B = src.source.reagents.reagent_list["blood"]
if (!B.pathogens.len)
boutput(usr, "The inserted blood sample is clean, there is nothing to isolate.")
maybegin = 0
else if (!src.target)
boutput(usr, "You cannot begin isolation without a target receptacle.")
maybegin = 0
if (maybegin)
src.visible_message("The centrifuge powers up and begins the isolation process.", "You hear a machine powering up.")
src.on = 1
src.icon_state = "centrifuge1"
var/obj/item/bloodslide/S = src.source
var/datum/reagent/blood/pathogen/P = new
var/datum/reagent/blood/B = src.source.reagents.reagent_list["blood"]
if (src.isolated)
P.pathogens = list(src.isolated.pathogen_uid = src.isolated)
else
P.pathogens = B.pathogens.Copy()
P.volume = 5
if (!(src in processing_items))
processing_items.Add(src)
src.process_pathogen = P
src.process_source = S
counter = 25
src.attack_hand(usr)
attackby(var/obj/item/O as obj, var/mob/user as mob)
if (istype(O, /obj/item/bloodslide))
if (src.source)
boutput(user, "There is already a blood slide in the machine.")
return
else
src.source = O
O.loc = src
O.master = src
O.layer = src.layer
src.contents += O
if (user.client)
user.client.screen -= O
user.u_equip(O)
boutput(user, "You insert the blood slide into the machine.")
if (src.source.blood && src.source.blood.pathogens.len == 1)
var/uid = src.source.blood.pathogens[1]
src.isolated = src.source.blood.pathogens[uid]
else
src.isolated = null
else if (istype(O, /obj/item/reagent_containers/glass/petridish))
if (src.target)
boutput(user, "There is already a petri dish in the machine.")
return
else
src.target = O
O.loc = src
O.master = src
O.layer = src.layer
src.contents += O
if (user.client)
user.client.screen -= O
user.u_equip(O)
boutput(user, "You insert the petri dish into the machine.")
process()
if (!src.on)
return
counter--
if (counter <= 0)
processing_items.Remove(src)
var/datum/reagent/blood/pathogen/P = src.process_pathogen
src.visible_message("The centrifuge beeps and discards the disfigured bloodslide.", "You hear a machine powering down.")
if (src.target.reagents.has_reagent("pathogen"))
var/datum/reagent/blood/pathogen/Q = src.target.reagents.reagent_list["pathogen"]
for (var/uid in P.pathogens)
var/datum/pathogen/PT = P.pathogens[uid]
Q.pathogens += uid
Q.pathogens[uid] = PT
else
src.target.reagents.reagent_list += "pathogen"
src.target.reagents.reagent_list["pathogen"] = P
P.holder = src.target.reagents
src.target.reagents.update_total()
src.target.icon_state = "petri1"
src.target.stage = 0
del(src.source)
src.source = null
src.isolated = null
src.on = 0
src.icon_state = "centrifuge0"
/obj/machinery/microscope
name = "Microscope"
icon = 'icons/obj/pathology.dmi'
icon_state = "microscope0"
desc = "A device which provides a magnified view of a culture in a petri dish."
var/obj/item/target = null
var/list/symptom_action_out = new/list()
var/list/symptom_action_in = new/list()
var/list/supp_action = new/list()
var/zoom = 0
anchored = 1
proc/message_parts(var/message)
var/cloc = findtext(message, ":")
if (cloc)
var/name = copytext(message, 1, cloc + 1)
var/data = copytext(message, cloc + 2)
return list(name, data)
else
return null
attack_hand(mob/user as mob)
if (src.target)
var/action = input("What would you like to do with the microscope?", "Microscope", "View [target]") in list("View [target]", "[src.zoom ? "Zoom Out" : "Zoom In"]", "Remove [target]", "Cancel")
if (get_dist(user.loc, src.loc) <= 1)
if (action == "View [target]")
if (zoom)
user.show_message("You look at the [target] through the microscope.")
if (istype(src.target, /obj/item/reagent_containers/glass/petridish))
var/obj/item/reagent_containers/glass/petridish/PD = target
if (PD.dirty)
user.show_message("The petri dish cannot be used for cultivating pathogens, due to: ")
user.show_message(PD.dirty_reason)
var/list/path_list = src.target.reagents.aggregate_pathogens()
var/pcount = path_list.len
if (pcount > 0)
var/uid
var/datum/pathogen/P
if (pcount > 1)
var/list/names = new/list()
for (uid in path_list)
P = path_list[uid]
names += P.name
names += "Cancel"
var/name = input("Which pathogen?", "Microscope", "Cancel") in names
if (name == "Cancel")
return
for (uid in path_list)
P = path_list[uid]
if (P.name == name)
break
else
uid = path_list[1]
P = path_list[uid]
user.show_message("Apparent features of the pathogen:")
var/lines = 1
user.show_message(P.suppressant.may_react_to())
for (var/datum/pathogeneffects/E in P.effects)
var/res = E.may_react_to()
if (res)
lines++
user.show_message("[res]")
if (!lines)
user.show_message("You cannot see anything out of the ordinary.")
if (src.symptom_action_in.len)
user.show_message("You can observe in the [target]:")
for (var/act in src.symptom_action_in)
var/list/actl = message_parts(act)
if (actl[1] == P.name)
user.show_message("[actl[2]]")
if (src.supp_action[P.name])
user.show_message("[src.supp_action[P.name]]")
else
user.show_message("The [target] is empty.")
else
var/list/path_list = src.target.reagents.aggregate_pathogens()
user.show_message("You look at the [target] through the microscope.")
var/pcount = path_list.len
if (pcount > 0)
var/uid
var/datum/pathogen/P
if (pcount > 1)
var/list/names = new/list()
for (uid in path_list)
P = path_list[uid]
names += P.name
names += "Cancel"
var/name = input("Which pathogen?", "Microscope", "Cancel") in names
if (name == "Cancel")
return
for (uid in path_list)
P = path_list[uid]
if (P.name == name)
break
else
uid = path_list[1]
P = path_list[uid]
user.show_message("The pathogen appears to be consistent with the strain [P.name_base]")
user.show_message("The pathogen appears to be composed of [P.desc].")
if (src.symptom_action_out.len)
user.show_message("You can observe in the [target]:")
for (var/act in src.symptom_action_out)
var/list/actl = message_parts(act)
if (actl[1] == P.name)
user.show_message("[actl[2]]")
if (src.supp_action[P.name])
user.show_message("[src.supp_action[P.name]]")
else
user.show_message("The [target] is empty.")
else if (action == "Zoom Out")
zoom = 0
icon_state = "microscope1"
user.show_message("The microscope is now zoomed out.")
else if (action == "Zoom In")
zoom = 1
icon_state = "microscope3"
user.show_message("The microscope is now zoomed in.")
else if (action == "Remove [target]")
user.show_message("You remove the [target] from the microscope.")
src.target.loc = src.loc
src.target.layer = initial(src.target.layer)
src.target.master = null
icon_state = zoom ? "microscope2" : "microscope0"
src.contents -= src.target
src.target = null
attackby(var/obj/item/O as obj, var/mob/user as mob)
if (istype(O, /obj/item/reagent_containers/glass/petridish) || istype(O, /obj/item/bloodslide))
if (src.target)
boutput(user, "There is already a [target] on the microscope.")
return
else
src.target = O
O.loc = src
O.master = src
O.layer = src.layer
src.contents += O
if (user.client)
user.client.screen -= O
user.u_equip(O)
src.icon_state = zoom ? "microscope3" : "microscope1"
boutput(user, "You insert the [O] into the microscope.")
else if (istype(O, /obj/item/reagent_containers/dropper))
if (src.target && istype(src.target, /obj/item/reagent_containers/glass/petridish))
if (O.reagents.total_volume > 0)
user.visible_message("[user] drips some of the contents of the dropper into the petri dish.", "You drip some of the contents of the dropper into the petri dish.")
var/list/path_list = src.target.reagents.aggregate_pathogens()
for (var/rid in O.reagents.reagent_list)
var/datum/reagent/R = O.reagents.reagent_list[rid]
if (R.volume < 1)
continue
for (var/uid in path_list)
var/datum/pathogen/P = path_list[uid]
var/act = P.suppressant.react_to(R.id)
if (act != null)
if (!(P.name in src.supp_action))
src.supp_action += P.name
if (P.curable_by_suppression)
act += " The culture appears to be severely damaged by the suppressing agent."
src.supp_action[P.name] = act
spawn(100)
src.supp_action -= P.name
for (var/datum/pathogeneffects/E in P.effects)
var/a_in = "[P.name]: " + E.react_to(R.id, 1)
var/a_out = "[P.name]: " + E.react_to(R.id, 0)
if (a_in && !(a_in in src.symptom_action_in))
src.symptom_action_in += a_in
spawn(100)
src.symptom_action_in -= a_in
if (a_out && !(a_out in src.symptom_action_out))
src.symptom_action_out += a_out
spawn(100)
src.symptom_action_out -= a_out
#define PATHOGEN_MANIPULATOR_STATE_MAIN 0
#define PATHOGEN_MANIPULATOR_STATE_LOADER 1
#define PATHOGEN_MANIPULATOR_STATE_MANIPULATE 2
#define PATHOGEN_MANIPULATOR_STATE_SPLICE 3
#define PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION 4
#define PATHOGEN_MANIPULATOR_STATE_TESTER 5
#define SEND_SLOT_LOAD_INFO gui.sendToSubscribers({"{"dnaDetails":[src.slots2json()], "loadedDna":[src.pathogen2json(src.manip.loaded)]}"}, "setUIState")
#define PA_SUCCESS 1
#define PA_UNKNOWN 2
#define PA_FAIL 4
/datum/pathobank
var/list/known_sequences = list()
var/certainty = 0
var/list/assigned_names = list()
var/list/transient_sequences = list()
/obj/machinery/computer/pathology
name = "Pathology Research"
icon = 'icons/obj/computer.dmi'
icon_state = "pathology"
desc = "A bulky machine used to control the pathogen manipulator."
var/obj/machinery/pathogen_manipulator/manip = null
var/datum/pathobank/db = new
var/predictive_data = ""
var/datum/spyGUI/gui = null
New()
..()
gui = new("html/pathoComp.html", "pathology", "size=900x800", src)
gui.validate_user = 1
spawn(50)
rescan()
proc/rescan()
for (var/obj/machinery/pathogen_manipulator/P in orange(1, src))
src.manip = P
P.comp = src
break
attack_hand(var/mob/user as mob)
..()
show_interface(user)
proc/show_interface(var/mob/user as mob)
if(!src.manip)
rescan()
if(!src.manip)
user.show_text("The [src] flashes an assertive \"NO CONNECTION\" message. Looks like it wants a pathogen manipulator.", "red")
return
gui.displayInterface(user, initUI())
if(src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
sendSpliceInfo(1)
sendAnalysisData()
/*
user << browse(grabResource("html/PathoComp.html"), "window=pathology;size=900x800")
sendData(user, initUI(), "setUIState")
*/
proc/initUI()
var/out = {"{"src":"\ref[src]","actPage":[src.manip.machine_state],"exposed":[src.manip.exposed],"loadedDna":[pathogen2json(src.manip.loaded)],"dnaDetails":[slots2json()],"splice":{"selected":[src.manip.splicesource]}}"}
return out
proc/pathogen2json(var/datum/pathogendna/PDNA)
if(!PDNA)
return "null"
var/splicing = (PDNA == src.manip.loaded && (!PDNA.valid || src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION))
return {"{"seq":"[PDNA.seqnumeric + PDNA.seqsplice]","pathogenName":"[PDNA.reference.name]","pathogenType":"[PDNA.reference.body_type.singular]","isSplicing":[splicing]}"}
proc/slots2json()
if(!src.manip) return "\[null,null,null]"
var/seqs = "\["
var/delimiter = ""
for(var/i = 1; i <= src.manip.slots.len; i++)
seqs +="[delimiter][pathogen2json(src.manip.slots[i])]"
delimiter=","
seqs += "]"
return seqs
proc/sendSpliceInfo(var/use_cache = 0)
var/tOut = ""
var/sOut = ""
if(use_cache)
for(var/i = 1; i <= src.manip.cache_target.len; i++)
tOut += src.manip.cache_target[i]
for(var/i = 1; i <= src.manip.cache_source.len; i++)
sOut += src.manip.cache_source[i]
else
if(src.manip.loaded)
tOut = src.manip.loaded.seqsplice
if(src.manip.splicesource && src.manip.slots[src.manip.splicesource])
var/datum/pathogendna/P = src.manip.slots[src.manip.splicesource]
sOut = P.seqsplice
tOut = length(tOut) > 0 ? "\"[tOut]\"" : "null"
sOut = length(sOut) > 0 ? "\"[sOut]\"" : "null"
gui.sendToSubscribers({"{"splice":{"source":[sOut],"target":[tOut],"pred":[predictive_data],"selSource":[src.manip.sel_source],"selTarget":[src.manip.sel_target],"selected":[src.manip.splicesource]}}"}, "setUIState")
proc/sendAnalysisData()
var/out = {"{"analysis":{"curr":"[src.manip.analysis]","predeffect":[db.certainty],"buttons":"[jointext(src.manip.analysis_list,"")]""}
if(src.manip.last_analysis)
out += {","prev":[src.manip.last_analysis]"}
out += "}}"
gui.sendToSubscribers(out, "setUIState")
Topic(href, href_list)
if ( ..() )
gui.unsubscribeTarget(usr)
return
if (href_list["showknown"])
var/json = "\["
var/delimit = ""
// "
';
usr << browse(op, "window=pathology_ks;size=300x500")
if (href_list["setstate"])
var/state = text2num(href_list["newstate"])
if(state != null && state >= 0 && state <= 5 && state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
//Received valid input, it's within bounds and it's not moving to or from a protected state (splicing in progress)
src.manip.machine_state = state
gui.sendToSubscribers({"{"actPage":[state]}"}, "setUIState")
if (href_list["analysisclear"])
src.manip.analysis = null
sendAnalysisData()
if (href_list["analysisdestroy"])
if (src.manip.loaded)
src.manip.analysis_list.len = 0
var/list/bits = src.manip.loaded.explode()
for (var/bit in bits)
if (bit != "|")
src.manip.analysis_list += bit
qdel(src.manip.loaded)
src.manip.loaded = null
visible_message("The manipulator ejects the empty vial.")
new /obj/item/reagent_containers/glass/vial(get_turf(src.manip))
SEND_SLOT_LOAD_INFO
sendAnalysisData()
if (href_list["analysisappend"])
if (length(src.manip.analysis) >= 15)
return
var/id = text2num(href_list["analysisappend"])
if(id != null && id >= 0)
id++ //JS sent a zero-based ID
if (id > 0 && src.manip.analysis_list.len >= id) //We want the index to be in bounds now.
var/element = src.manip.analysis_list[id]
src.manip.analysis_list.Cut(id, id+1)
if (!src.manip.analysis)
src.manip.analysis = ""
src.manip.analysis += element
sendAnalysisData()
if (href_list["analysisdo"])
if (!src.manip.analysis)
return
var/tlen = length(src.manip.analysis)
if (tlen < 3)
return
var/analyzed = src.manip.analysis
if (tlen > 15)
analyzed = copytext(analyzed, 1, 16)
tlen = 15
var/bits = tlen / 3
var/acc = ""
//Result variables
var/stable = 0
var/transient = 0
var/seqs = "\["
var/conf = "\["
var/delim = ""
if (analyzed in pathogen_controller.UID_to_symptom)
stable = 1
if (!(analyzed in db.known_sequences))
db.known_sequences[analyzed] = stable
db.certainty += (stable ? 8 : 4) * (100 - db.certainty) / 100
for (var/i = 1, i <= bits, i++)
var/curr = copytext(analyzed, (i - 1) * 3 + 1, i * 3 + 1)
acc += curr
var/acc_len = length(acc)
var/total = 0
var/match = 0
for (var/dna in pathogen_controller.UID_to_symptom)
var/dnalen = length(dna)
if (dnalen >= acc_len)
total++
if (dnalen == acc_len)
if (dna == acc)
match++
else
total--
else
if (copytext(dna, 1, acc_len + 1) == acc)
match++
var/ratio = 0
if (total)
ratio = match / total
seqs += "[delim]\"[curr]\""
conf += "[delim][ratio]"
delim = ","
/*
end_part += "[curr] "
*/
if (i == bits && match && (!stable || match > 1))
//output += "Transient: Yes "
transient = 1
db.transient_sequences[analyzed] = "Yes"
else if (i == bits)
//output += "Transient: No "
transient = -1
db.transient_sequences[analyzed] = "No"
seqs += "]"
conf += "]"
if (!stable)
src.manip.analysis = null
stable = -1
var/output = {"{"valid":1,"stable":[stable],"trans":[transient],"seqs":[seqs],"conf":[conf]}"}
src.manip.last_analysis = output
//gui.sendToSubscribers(output, "handleAnalysisTestCallback")
sendAnalysisData()
if (href_list["rescan"])
rescan()
if (href_list["exchange"])
if (src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_MANIPULATE)
var/swap = src.manip.loaded
var/slotid = text2num(href_list["exchange"])
src.manip.loaded = src.manip.slots[slotid]
if (src.manip.splicesource == slotid)
src.manip.splicesource = 0
src.manip.slots[slotid] = swap
SEND_SLOT_LOAD_INFO
if (href_list["load"])
if (src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_MANIPULATE)
var/slotid = text2num(href_list["load"])
src.manip.loaded = src.manip.slots[slotid]
if (src.manip.splicesource == slotid)
src.manip.splicesource = 0
src.manip.slots[slotid] = null
SEND_SLOT_LOAD_INFO
if (href_list["cancel"])
src.manip.splicesource = 0
gui.sendToSubscribers({"{"splice":{"source":[src.manip.splicesource]}}"}, "setUIState")
if (href_list["expose"])
if (src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_MANIPULATE)
var/slotid = text2num(href_list["expose"])
src.manip.exposed = slotid
if (src.manip.slots[src.manip.exposed])
src.manip.icon_state = "manipulatore"
else
src.manip.icon_state = "manipulator"
gui.sendToSubscribers({"{"exposed":[src.manip.exposed]}"}, "setUIState")
if (href_list["splice"])
var/slotid = minmax(text2num(href_list["splice"]), 1, src.manip.slots.len)
src.manip.splicesource = slotid
gui.sendToSubscribers({"{"splice":{"selected":[src.manip.splicesource]}}"}, "setUIState")
if (href_list["remove"])
if (src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_MANIPULATE)
var/slotid = text2num(href_list["remove"])
if (src.manip.splicesource == slotid)
src.manip.splicesource = 0
src.manip.slots[slotid] = null
gui.sendToSubscribers({"{"splice":{"source":[src.manip.splicesource]}, "dnaDetails":[slots2json()]}"}, "setUIState")
if (href_list["save"])
if (src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_MANIPULATE)
var/slotid = text2num(href_list["save"])
src.manip.slots[slotid] = src.manip.loaded
src.manip.loaded = null
SEND_SLOT_LOAD_INFO
if(href_list["manip"])
var/mut_type
switch(href_list["manip"])
if("mut")
mut_type = "mutativeness"
if("mts")
mut_type = "mutation_speed"
if("adv")
mut_type = "advance_speed"
if("mal")
mut_type = "maliciousness"
if("sth")
mut_type = "suppression_threshold"
else
return
var/dir = text2num(href_list["dir"])
if(mut_type && dir && (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_MANIPULATE))
var/act = src.manip.loaded.manipulate(mut_type, dir)
var/out
if (act == 0)
src.manip.visible_message("The DNA is destabilized and destroyed by the radiation.")
out= {"{"success":0}"}
else if (act == -1)
src.manip.visible_message("The structure of the DNA appears to fundamentally change.")
if(!out) out = {"{"newseq":"[src.manip.loaded.seqnumeric + src.manip.loaded.seqsplice]","success":1}"}
gui.sendToSubscribers(out, "handleManipCallback")
if (href_list["eject"])
if (src.manip.exposed && src.manip.slots[src.manip.exposed] && src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
var/datum/reagent/blood/pathogen/P = new
var/datum/pathogendna/D = src.manip.slots[src.manip.exposed]
var/datum/pathogen/PT = unpool(/datum/pathogen)
PT.setup(0, D.reference)
PT.dnasample = D
P.pathogens += PT.pathogen_uid
P.pathogens[PT.pathogen_uid] = PT
P.volume = 2
var/obj/item/reagent_containers/glass/vial/vial = new
vial.reagents.reagent_list[P.id] = P
vial.reagents.total_volume = 2
vial.loc = src.manip.loc
vial.icon_state = "vial1"
src.manip.slots[src.manip.exposed] = null
src.manip.icon_state = "manipulator"
SEND_SLOT_LOAD_INFO
if (href_list["insert"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
var/offset = text2num(href_list["insert"])
var/seq = src.manip.cache_source[src.manip.sel_source]
for (var/i = src.manip.sel_source, i < src.manip.cache_source.len, i++)
src.manip.cache_source[i] = src.manip.cache_source[i+1]
src.manip.cache_source.Cut(src.manip.cache_source.len)
src.manip.cache_target += "#IN"
for (var/i = src.manip.cache_target.len, i > src.manip.sel_target + 1 + offset, i--)
src.manip.cache_target[i] = src.manip.cache_target[i-1]
src.manip.cache_target[src.manip.sel_target + 1 + offset] = seq
//src.manip.sel_target--
src.manip.sel_source--
if (src.manip.sel_source < 1)
src.manip.sel_source = 1
predictive_analysis()
if(href_list["splicesel"])
var/i = text2num(href_list["splicesel"])
var/t = text2num(href_list["target"])
if(t)
i = minmax(i+1, 1, src.manip.cache_target.len)
src.manip.sel_target = i
gui.sendToSubscribers({"{"splice":{"selTarget":[i]}}"}, "setUIState")
else
i = minmax(i+1, 1, src.manip.cache_source.len)
src.manip.sel_source = i
gui.sendToSubscribers({"{"splice":{"selSource":[i]}}"}, "setUIState")
if(href_list["splicemod"])
var/iRel = text2num(href_list["rel"]) //The operation to perform, 0 = remove, -1 = insert before, 1 = insert after
var/iPos = text2num(href_list["pos"]) //The target index
var/sPos = text2num(href_list["SourcePos"]) //The source index
if(iRel == null || iPos == null || (sPos == null && iRel != 0) )
return
iRel = minmax(iRel, -1, 1)
//Increase the positions by one since they are 0-indexed JS.
iPos = minmax(iPos+1, 1, src.manip.cache_target.len)
sPos = minmax(sPos+1, 1, src.manip.cache_source.len)
if(iRel == 0) //Remove
if(src.manip.cache_target.len)
src.manip.cache_target.Cut(iPos,iPos+1)
src.manip.sel_target = min(iPos, src.manip.cache_target.len) //Ensure the new selected target is within bounds
else //Insert
iRel = max(iRel,0) //In case we're inserting before we don't want to subtract from the target index
if(src.manip.cache_source.len)
var/newpos = minmax(iPos + iRel, 1, src.manip.cache_target.len+1) //Set the position to insert at
src.manip.cache_target.Insert(newpos, src.manip.cache_source[sPos]) //Do the insertion
src.manip.sel_target = min(iPos + iRel, src.manip.cache_target.len) //Shift the selection to the newly inserted component
src.manip.cache_source.Cut(sPos, sPos+1) //Remove the DNA component from the source
src.manip.sel_source = min(sPos, src.manip.cache_source.len) //Ensure the last position in the array is selected.
predictive_analysis()
sendSpliceInfo(1)
if (href_list["beginsplice"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICE && src.manip.loaded && src.manip.splicesource && src.manip.slots[src.manip.splicesource])
src.manip.cache_target = src.manip.loaded.explode()
var/datum/pathogendna/P = src.manip.slots[src.manip.splicesource]
src.manip.cache_source = P.explode()
src.manip.machine_state = PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION
src.manip.icon_state = "manipulator1"
predictive_data = 1
SEND_SLOT_LOAD_INFO
sendSpliceInfo(0)
/*
if (href_list["target"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
var/offset = text2num(href_list["target"])
if (offset > 0)
if (src.manip.sel_target < src.manip.cache_target.len)
src.manip.sel_target++
else
if (src.manip.sel_target > 1)
src.manip.sel_target--
if (href_list["source"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
var/offset = text2num(href_list["source"])
if (offset > 0)
if (src.manip.sel_source < src.manip.cache_source.len)
src.manip.sel_source++
else
if (src.manip.sel_source > 1)
src.manip.sel_source--
if (href_list["jumpt"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
src.manip.sel_target = text2num(href_list["jumpt"])
if (href_list["jumps"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
src.manip.sel_source = text2num(href_list["jumps"])
*/
if (href_list["seqremove"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
for (var/i = src.manip.sel_target, i < src.manip.cache_target.len, i++)
src.manip.cache_target[i] = src.manip.cache_target[i+1]
src.manip.cache_target.Cut(src.manip.cache_target.len)
src.manip.sel_target--
predictive_analysis()
if (href_list["splicefinish"])
if (src.manip.machine_state == PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
src.manip.icon_state = "manipulator"
var/datum/pathogendna/L = src.manip.loaded
var/oldname = L.reference.name
var/success = 0
L.implode(src.manip.cache_target)
if (L.reevaluate())
var/list/seqs = L.get_sequences()
for (var/s in seqs)
if (s in db.known_sequences)
continue
db.known_sequences[s] = 1
db.certainty += 5 * (100 - db.certainty) / 100
db.certainty = min(db.certainty, 100)
if(!s in db.transient_sequences)
db.transient_sequences[s] = "UNK"
boutput(usr, "The DNA sequence is assembled by the manipulator.")
src.manip.loaded = L
if (prob(10))
if (prob(75))
boutput(usr, "The splicing session is completed imperfectly. The DNA sequence mutates.")
src.manip.loaded.reference.mutate()
src.manip.loaded.recalculate()
src.manip.loaded.reverse_engineer()
success=1
else
boutput(usr, "The splicing session is completed imperfectly. The DNA sequence is lost.")
qdel(src.manip.loaded)
new /obj/item/reagent_containers/glass/vial(get_turf(src.manip)) //Quit eating vials you fuck -Spy
else
boutput(usr, "The splicing session is concluded perfectly. The DNA sequence remains intact.")
success=1
src.manip.loaded.move_mutation()
if (src.manip.loaded && !src.manip.loaded.disposed)
src.manip.loaded.reference.cdc_announce(usr)
var/datum/pathogendna/source = src.manip.slots[src.manip.splicesource]
logTheThing("pathology", usr, null, "splices pathogen [source.reference.name] into [oldname] creating [src.manip.loaded.reference.name].")
else
boutput(usr, "The DNA sequence is assembled by the manipulator, but it collapses!")
src.manip.loaded = null
new /obj/item/reagent_containers/glass/vial(get_turf(src.manip)) //Quit eating vials you fuck -Spy
qdel(src.manip.slots[src.manip.splicesource])
src.manip.slots[src.manip.splicesource] = null
src.manip.splicesource = 0
src.manip.machine_state = PATHOGEN_MANIPULATOR_STATE_MAIN
visible_message("The manipulator ejects the empty vial.")
new /obj/item/reagent_containers/glass/vial(get_turf(src.manip))
var/datum/pathogendna/PDNA = src.manip.loaded
if(success && PDNA)
gui.sendToSubscribers({"{"newseq":"[PDNA.seqnumeric + PDNA.seqsplice]","success":1}"}, "handleSpliceCompletionCallback")
else
gui.sendToSubscribers({"{"success":0}"}, "handleSpliceCompletionCallback")
SEND_SLOT_LOAD_INFO
if (href_list["lock"])
if (src.manip.machine_state != PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION)
src.manip.exposed = 0
src.manip.icon_state = "manipulator"
gui.sendToSubscribers({"{"exposed":[src.manip.exposed]}"}, "setUIState")
proc/predictive_analysis()
if (!prob(db.certainty))
predictive_data = PA_UNKNOWN //"Insufficient data, predictive analysis failed"
else
if (prob(100 - db.certainty))
if (prob(50))
predictive_data = PA_SUCCESS //"Sequence suspected to be stable"
else
predictive_data = PA_FAIL //"Sequence suspected to be unstable"
else
var/datum/pathogendna/L = src.manip.loaded.clone()
L.implode(src.manip.cache_target)
var/list/seq = L.get_sequences()
if (!seq.len)
predictive_data = PA_FAIL //"Sequence suspected to be unstable"
return
for (var/s in seq)
if (s in db.known_sequences)
if (!db.known_sequences[s])
predictive_data = PA_FAIL //"Sequence suspected to be unstable"
return
else
if (prob(db.certainty) || prob(50))
if (!(s in pathogen_controller.UID_to_symptom))
predictive_data = PA_FAIL//"Sequence suspected to be unstable"
return
predictive_data = PA_SUCCESS //"Sequence suspected to be stable"
#undef SEND_SLOT_LOAD_INFO
#undef PA_SUCCESS
#undef PA_UNKNOWN
#undef PA_FAIL
/obj/machinery/pathogen_manipulator
name = "Pathogen Manipulator"
icon = 'icons/obj/pathology.dmi'
icon_state = "manipulator"
desc = "A large, softly humming machine."
density = 1
anchored = 1
var/machine_state = 0
var/sel_target = 1
var/sel_source = 1
var/list/cache_target = null
var/list/cache_source = null
var/list/analysis_list = list()
var/analysis = null
var/last_analysis = null
var/splicesource = 0
var/exposed = 0
var/datum/pathogendna/loaded = null
var/list/datum/pathogendna/slots[3]
var/obj/item/reagent_containers/container = null
var/obj/machinery/computer/pathology/comp = null
New()
flags |= NOSPLASH
attackby(var/obj/item/O as obj, var/mob/user as mob)
if (!exposed)
user.show_message("The manipulator has no exposed slots.")
return
if (slots[exposed])
user.show_message("The currently exposed slot on the manipulator is occupied.")
return
if (!istype(O, /obj/item/reagent_containers/glass/vial))
user.show_message("The slots on the manipulator are designed so that only vials will fit.")
return
if (!O.reagents.has_reagent("pathogen"))
user.show_message("The vial does not contain a viable pathogen sample, and is rejected by the machine.")
return
if (O.reagents.reagent_list.len > 1)
user.show_message("The machine rejects the sample, as it contains foreign chemical samples.")
return
var/datum/reagent/blood/pathogen/P = O.reagents.reagent_list["pathogen"]
if (P.pathogens.len > 1)
user.show_message("The vial contains multiple pathogen samples, and is rejected by the machine.")
return
if (P.pathogens.len == 0)
user.show_message("The vial does not contain a viable pathogen sample, and is rejected by the machine.")
return
if (P.volume < 2)
user.show_message("Too small sample size. At least 2 units of pathogen required.")
return
var/uid = P.pathogens[1]
var/datum/pathogen/PT = P.pathogens[uid]
//boutput(user, "Valid. Contains pathogen ([P.volume] units with pathogen [PT.name]. Slot is [exposed]. DNA: [PT.dnasample]")
if (!PT.dnasample)
PT.dnasample = new(PT) // damage control
logTheThing("pathology", usr, null, "Pathogen [PT.name] (\ref[PT]) had no DNA. (this is a bug)")
slots[exposed] = PT.dnasample.clone()
O.reagents.del_reagent("pathogen")
user.u_equip(O)
qdel(O)
user.show_message("You insert the vial into the machine.")
icon_state = "manipulatore"
if (comp)
comp.gui.sendToSubscribers({"{"dnaDetails":[src.comp.slots2json()]}"}, "setUIState")
#undef PATHOGEN_MANIPULATOR_STATE_MAIN
#undef PATHOGEN_MANIPULATOR_STATE_LOADER
#undef PATHOGEN_MANIPULATOR_STATE_MANIPULATE
#undef PATHOGEN_MANIPULATOR_STATE_SPLICE
#undef PATHOGEN_MANIPULATOR_STATE_SPLICING_SESSION
/obj/item/synthmodule
name = "Synth-O-Matic module"
desc = "A module that integrates with a Synth-O-Matic machine."
icon = 'icons/obj/pathology.dmi'
icon_state = "synthmodule"
var/id = "bad"
proc/received(obj/machinery/synthomatic/S)
return
afterattack(obj/target, mob/user , flag)
if (istype(target, /obj/machinery/synthomatic))
return
..(target, user, flag)
/obj/item/synthmodule/vaccine
name = "Synth-O-Matic Vaccine module"
desc = "A module that allows the Synth-O-Matic machine to create vaccines."
id = "vaccine"
/obj/item/synthmodule/upgrader
name = "Synth-O-Matic Efficiency module"
desc = "A module that allows the Synth-O-Matic machine to synthesize more anti-pathogenic agents from a single sample."
id = "upgrade"
/obj/item/synthmodule/assistant
name = "Synth-O-Matic Assistant module"
desc = "A module that assists in creating cure for pathogens for the Synth-O-Matic machine."
id = "assistant"
/obj/item/synthmodule/synthesizer
name = "Synth-O-Matic Antiagent module"
desc = "A module which allows the Synth-O-Matic to synthesize an anti-pathogen agent on the fly."
id = "synthesizer"
/obj/item/synthmodule/virii
name = "Synth-O-Matic Virii module"
desc = "A module that allows the Synth-O-Matic to internally generate cures to virii."
id = "virii"
/obj/item/synthmodule/bacteria
name = "Synth-O-Matic Bacteria module"
desc = "A module that allows the Synth-O-Matic to internally generate cures to bacteria."
id = "bacteria"
/obj/item/synthmodule/fungi
name = "Synth-O-Matic Fungi module"
desc = "A module that allows the Synth-O-Matic to internally generate cures to fungi."
id = "fungi"
/obj/item/synthmodule/parasite
name = "Synth-O-Matic Parasite module"
desc = "A module that allows the Synth-O-Matic to internally generate cures to parasitic diseases, using biocides."
id = "parasite"
/obj/item/synthmodule/gmcell
name = "Synth-O-Matic Mutatis module"
desc = "A module that allows the Synth-O-Matic to internally generate cures to great mutatis cell diseases."
id = "gmcell"
/obj/item/synthmodule/radiation
name = "Synth-O-Matic Irradiation module"
desc = "A module that allows the Synth-O-Matic to generate cure through irradiation, instead of chemicals."
id = "radiation"
/obj/machinery/synthomatic
name = "Synth-O-Matic 6.5.535"
desc = "The leading technological assistant in synthesizing cure for certain pathogens."
icon = 'icons/obj/pathology.dmi'
icon_state = "synth1"
density = 1
anchored = 1
var/list/obj/item/reagent_containers/glass/vial/vials[5]
var/obj/item/reagent_containers/glass/beaker/antiagent = null
var/obj/item/reagent_containers/glass/beaker/suppressant = null
var/list/obj/item/synthmodule/modules = list()
var/maintenance = 0
var/machine_state = 0
var/sel_vial = 0
New()
src.reagents = new(100)
src.reagents.my_atom = src
flags |= NOSPLASH
if (!pathogen_controller || !pathogen_controller.cure_bases || !pathogen_controller.cure_bases.len)
spawn(20)
for (var/C in pathogen_controller.cure_bases)
src.reagents.add_reagent(C, 1)
else
for (var/C in pathogen_controller.cure_bases)
src.reagents.add_reagent(C, 1)
src.add_module(new /obj/item/synthmodule/virii())
src.add_module(new /obj/item/synthmodule/bacteria())
src.add_module(new /obj/item/synthmodule/parasite())
src.add_module(new /obj/item/synthmodule/gmcell())
attack_hand(var/mob/user as mob)
..()
show_interface(user)
proc/add_module(var/obj/item/synthmodule/M)
if (has_module(M))
boutput(usr, "The [name] already has that kind of module.")
return 0
else
modules[M.id] = M
M.loc = src
M.received(src)
return 1
proc/has_module(var/id)
if (src.modules.len && (id in src.modules) && src.modules[id])
return 1
return 0
attackby(var/obj/item/O as obj, var/mob/user as mob)
if (istype(O, /obj/item/reagent_containers/glass/vial))
var/done = 0
for (var/i = 1, i <= 5, i++)
if (!(vials[i]))
done = 1
vials[i] = O
user.u_equip(O)
O.loc = src
O.master = src
user.client.screen -= O
break
if (!done)
boutput(usr, "The machine cannot hold any more vials.")
else
boutput(usr, "You insert the vial into the machine.")
show_interface(user)
return
if (istype(O, /obj/item/reagent_containers/glass/beaker))
var/action = input("Which slot?", "Synth-O-Matic", "Cancel") in list("Anti-Agent", "Suppressant", "Cancel")
if (action == "Anti-Agent")
if (!(usr in range(1)))
boutput(usr, "You must be near the machine to do that.")
return
if (usr.equipped() != O)
return
if (!antiagent)
antiagent = O
user.u_equip(O)
O.loc = src
O.master = src
user.client.screen -= O
boutput(usr, "You insert the beaker into the machine.")
show_interface(user)
else
boutput(usr, "That slot is already occupied!")
else if (action == "Suppressant")
if (!(usr in range(1)))
boutput(usr, "You must be near the machine to do that.")
return
if (usr.equipped() != O)
return
if (!suppressant)
suppressant = O
user.u_equip(O)
O.loc = src
O.master = src
user.client.screen -= O
boutput(usr, "You insert the beaker into the machine.")
show_interface(user)
else
boutput(usr, "That slot is already occupied!")
return
if (istype(O, /obj/item/screwdriver))
if (machine_state)
boutput(usr, "You cannot do that while the machine is working.")
return
if (!maintenance)
boutput(usr, "You open the maintenance panel on the Synth-O-Matic.")
icon_state = "synthp"
maintenance = 1
else
boutput(usr, "You close the maintenance panel on the Synth-O-Matic.")
icon_state = "synth1"
maintenance = 0
return
if (istype(O, /obj/item/synthmodule))
if (maintenance)
if (add_module(O))
boutput(user, "You insert the [O] into the machine.")
O.master = src
user.client.screen -= O
user.u_equip(O)
show_interface(user)
else
boutput(usr, "The machine already has the [O].")
else
boutput(usr, "You must open the maintenance panel first.")
return
..(O, user)
proc/show_interface(var/mob/user as mob)
var/output_text = ""
output_text += "SYNTH-O-MATIC 6.5.535 "
output_text += "\"Introducing the future in safe and controlled pathology science.\" "
output_text += " "
if (machine_state)
output_text += "The machine is currently working. Please wait."
else if (maintenance)
output_text += "Maintenance panel open - active modules "
for (var/module in modules)
var/obj/item/synthmodule/mod = modules[module]
output_text += "[mod.name] \[remove\] "
else
var/sane = 0
var/vaccinable = 0
var/body_name = null
var/module = null
output_text += "Active vial: "
if (sel_vial && vials[sel_vial])
var/obj/item/reagent_containers/glass/vial/V = vials[sel_vial]
if (V.reagents.has_reagent("pathogen"))
var/datum/reagent/blood/pathogen/R = V.reagents.reagent_list["pathogen"]
if (R.pathogens.len > 1)
output_text += "#[sel_vial] [V.name] (ERROR: contains multiple pathogen samples)
"
else if (!R.pathogens.len)
output_text += "#[sel_vial] [V.name] (empty)
"
else
var/uid = R.pathogens[1]
var/datum/pathogen/P = R.pathogens[uid]
sane = 1
vaccinable = P.body_type.vaccination
body_name = P.body_type.plural
module = P.body_type.module_id
output_text += "#[sel_vial] [V.name] (singular sample of strain [P.name_base]) "
if (has_module("assistant"))
var/units = P.suppression_threshold
output_text += " The assistant module suggests at least [units <= 5 ? 5 : units] unit(s) of one of the following suppressants for this pathogen: "
var/first = 1
for (var/supp in P.suppressant.cure_synthesis)
if (first)
first = 0
else
output_text += ", "
output_text += supp
output_text += "