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 -- *-*  <- Absolutely needed, do not delete.
 
 -- BeeAlverizer 1.1 fork of BeeAnalyzer 4
 -- Original code by Direwolf20
 -- Hotfixes by Mandydax, Mikeyhun and MaaadMike
 
 -- Major overhaul and rewrite to make work without turtle by Damaged
 
 
 -- JSON lib located at http://pastebin.com/jy3QenZn save as JSON.lua
--- Be careful of case
+-- Be careful of case
 
 if not fs.exists("JSON.lua") then
    shell.run("pastebin", "get", "jy3QenZn", "JSON.lua")
 end
 
 local JSON = (loadfile "JSON.lua")()
 JSON.strictTypes = true
 
 -- Build: http://users.on.net/~damageinc/Alveary%20placement.jpg
 
 -- Make sure you name this program "bee" (careful of case)
 
 -- Direction definitions.
 
 -- When looking at computer, what direction is it?
 -- Or simply put the direction in the label EG: bee1.west
 
 local alvearyDirection = "west"
 
 for i,case in pairs({ ".west", ".east", ".north", ".south" }) do
    if string.find(os.getComputerLabel(),case) then
       alvearyDirection = string.sub(case, 2)
       break
    end
 end
 print("I appear to be facing: "..alvearyDirection)
 local analyzerDirection
 local junkDirection
 
 if alvearyDirection == "west" then
    analyzerDirection = "south"
    junkDirection = "north"
 end
 if alvearyDirection == "north" then
    analyzerDirection = "west"
    junkDirection = "east"
 end
 if alvearyDirection == "east" then
    analyzerDirection = "north"
    junkDirection = "south"
 end
 if alvearyDirection == "south" then
    analyzerDirection = "east"
    junkDirection = "west"
 end
 
 
 
 
 
 
 
 -- attribute scoring for same species tie-breaking -----------------------------
 local droneTarget
 local princessSlot = 0
 alveary = peripheral.wrap("back")
 memoryChest = peripheral.wrap("top")
 local maxMem = memoryChest.getInventorySize()
 -- Fix for some versions returning bees.species.*
 function fixName(name)
    return name:gsub("bees%.species%.",""):gsub("^.", string.upper)
 end
 
 function getBeeData(i)
    return memoryChest.getStackInSlot(i)["beeInfo"]
 end
 
 function getPrimarySpecies(i)
    local thisBee = getBeeData(i)
    if thisBee["speciesPrimary"] ~= nil then
       return fixName(thisBee["speciesPrimary"])
    else
       return fixName(thisBee["active"]["species"])
    end
 end
 
 function getSecondarySpecies(i)
    if getBeeData(i)["speciesSecondary"] ~= nil then
       return fixName(getBeeData(i)["speciesSecondary"])
    else
       return fixName(getBeeData(i)["inactive"]["species"])
    end
 end
 
 scoresFertility = {
    [1] = 0.1,
    [2] = 0.2,
    [3] = 0.3,
    [4] = 0.4
 }
 scoresSpeed = {
    ["0.3"] = 0.01, -- Slowest
    ["0.6"] = 0.02, -- Slower
    ["0.8"] = 0.03, -- Slow
    ["1"]   = 0.04, -- Normal
    ["1.2"] = 0.05, -- Fast
    ["1.4"] = 0.06, -- Faster
    ["1.7"] = 0.07  -- Fastest
 }
 scoresAttrib = {
    diurnal       = 0.004,
    nocturnal     = 0.003,
    tolerantFlyer = 0.002,
    caveDwelling  = 0.0001
 }
 scoresTolerance = {
    ["NONE"]   = 0.00000,
    ["UP 1"]   = 0.00001,
    ["UP 2"]   = 0.00002,
    ["UP 3"]   = 0.00003,
    ["UP 4"]   = 0.00004,
    ["UP 5"]   = 0.00005,
    ["DOWN 1"] = 0.00001,
    ["DOWN 2"] = 0.00002,
    ["DOWN 3"] = 0.00003,
    ["DOWN 4"] = 0.00004,
    ["DOWN 5"] = 0.00005,
    ["BOTH 1"] = 0.00002,
    ["BOTH 2"] = 0.00004,
    ["BOTH 3"] = 0.00006,
    ["BOTH 4"] = 0.00008,
    ["BOTH 5"] = 0.00010
 }
 
 -- the bee graph ---------------------------------------------------------------
 
 bees = {}
 
 function addParent(parent, offspring)
    if bees[parent] then
       bees[parent].mutateTo[offspring] = true
       else
       bees[parent] = {
          --name = parent,
          score = nil,
          mutateTo = {[offspring]=true},
          mutateFrom = {}
       }
    end
 end
 
 function addOffspring(offspring, parentss)
    if bees[offspring] then
       for i, parents in ipairs(parentss) do
          table.insert(bees[offspring].mutateFrom, parents)
       end
       else
       bees[offspring] = {
          score = nil,
          mutateTo = {},
          mutateFrom = parentss
       }
    end
    for i, parents in ipairs(parentss) do
       for i, parent in ipairs(parents) do
          addParent(parent, offspring)
       end
    end
 end
 
 -- score bees that have no parent combinations as 1
 -- iteratively find the next bee up the line and increase the score
 function scoreBees()
    -- find all bees with no mutateFrom data
    local beeCount = 0
    local beeScore = 1
    for name, beeData in pairs(bees) do
       if #beeData.mutateFrom == 0 then
          beeData.score = beeScore
          else
          beeCount = beeCount + 1
       end
    end
    while beeCount > 0 do
       beeScore = beeScore * 2
       -- find all bees where all parent combos are scored
       for name, beeData in pairs(bees) do
          if not beeData.score then
             local scoreBee = true
             for i, beeParents in ipairs(beeData.mutateFrom) do
                local parent1 = bees[beeParents[1]]
                local parent2 = bees[beeParents[2]]
 
                if not parent1.score
                   or parent1.score == beeScore
                   or not parent2.score
                   or parent2.score == beeScore then
                   scoreBee = false
                   break
                end
             end
             if scoreBee then
                beeData.score = beeScore
                beeCount = beeCount - 1
             end
          end
       end
    end
 end
 
 -- produce combinations from 1 or 2 lists
 function choose(list, list2)
    local newList = {}
    if list2 then
       for i = 1, #list2 do
          for j = 1, #list do
             if list[j] ~= list[i] then
                table.insert(newList, {list[j], list2[i]})
             end
          end
       end
       else
       for i = 1, #list do
          for j = i, #list do
             if list[i] ~= list[j] then
                table.insert(newList, {list[i], list[j]})
             end
          end
       end
    end
    return newList
 end
 
 
 for key, value in pairs (alveary.getBeeBreedingData()) do
    addOffspring( fixName(value.result), {{ fixName(value.allele1), fixName(value.allele2) }} )
 end
 scoreBees()
 
 -- logging ---------------------------------------------------------------------
 
 local logFile = fs.open("bee.log", "w")
 function log(msg)
    msg = msg or ""
    logFile.write(tostring(msg))
    logFile.flush()
    io.write(msg)
 end
 function logLine(msg)
    msg = msg or ""
    logFile.write(msg.."\n")
    logFile.flush()
    io.write(msg.."\n")
 end
 
 function logTable(table)
    for key, value in pairs (table) do
       logLine(key .. " = " .. tostring(value))
    end
 end
 
 
 -- analyzing functions ---------------------------------------------------------
 
 function clearSystem()
    -- clear out alveary
    for i = 2,9 do
       memoryChest.pullItem(alvearyDirection,i)
    end
    -- clear out analyzer
    for i = 1, 12 do
       memoryChest.pullItem(analyzerDirection,i)
    end
 end
 
 function analyzeBees()
    princessSlot = 0
    logLine("analyzing bees...")
    memoryChest.condenseItems()
    local highestScore
    local highestScoreDrone
    for i,data in pairs(memoryChest.getAllStacks()) do
       data = memoryChest.getStackInSlot(i)
-      sleep(10)
+
          memoryChest.pushItem(junkDirection,i)
          print("P")
       else
          print("B")
          --print(JSON:encode(data["beeInfo"]))
          --print(data["beeInfo"]["isAnalyzed"])
          if data["beeInfo"]["isAnalyzed"] == false then
             memoryChest.pushItemIntoSlot(analyzerDirection,i,64,3)
             while memoryChest.pullItemIntoSlot(analyzerDirection,9,61,i) == 0 do sleep(1) end
          end
          if string.find(data["rawName"], "princess") then
             princessSlot = i
          end
       end
    end
 end
 
 local droneData
 droneData = { }
 
 function sortBees()
    droneData = { }
    if princessSlot ~= 0 then
       logLine("scoring drones...")
       for i,data in pairs(memoryChest.getAllStacks()) do
          if i ~= princessSlot then
             -- check for untargeted species
             if memoryChest.getStackInSlot(i) ~= nil and (not bees[getPrimarySpecies(i)].targeted or not bees[getSecondarySpecies(i)].targeted) then
-         -- check for untargeted species
+
-         if memoryChest.getStackInSlot(i) ~= nil and (not bees[getPrimarySpecies(i)].targeted or not bees[getSecondarySpecies(i)].targeted) then
+            else
-            memoryChest.pushItem(junkDirection,i)
+               droneData[i] = scoreBee(i)
                if droneData[i] == 0 then
-            if string.find(data["rawName"], "princess") then
+                  memoryChest.pushItem(junkDirection,i)
-               princessSlot = i
+                  droneData[i] = nil
                end
             end
          end
       end
       -- find the best drone
       logLine("sorting drones...")
       highestScore = 0
-            droneData[i] = scoreBee(i)
+
-            if droneData[i] == 0 then
+
             highestScore = beeScore
             highestScoreDrone = i
          end
       end
       printHeader()
       for i = 1, maxMem do
          if memoryChest.getStackInSlot(i) ~= nil then
             printBee(i)
          end
       end
    end
    logLine()
    return highestScoreDrone
 end
 
 function getBees()
    -- get bees from apiary
    log("waiting for bees.")
    local firstPass = true
    local highScore
    while true do
       local gotStuff = false
       for i = 3,9 do
          if memoryChest.pullItem(alvearyDirection,i) ~= 0 then
             gotStuff = true
          end
       end
       if gotStuff == true then
          break
       end
       if firstPass then
          firstPass = false
          logLine()
          logLine("First time waiting:")
          logLine("-compacting bees")
          for i = 1,maxMem do
             if droneData[i] ~= nil then
                if i ~= 1 then
                   for j = 1,i-1 do
                      if memoryChest.getStackInSlot(j) == nil then
                         memoryChest.swapStacks(i, j)
                         droneData[j] = droneData[i]
                         droneData[i] = nil
                         break
                      end
                   end
                end
             end
          end
          logLine("-resorting bees in chest")
          for i = 1,maxMem do
             if droneData[i] ~= nil then
                if memoryChest.getStackInSlot(i) ~= nil then
                   highScore = i
                   for j = i + 1, maxMem do
                      if memoryChest.getStackInSlot(j) ~= nil then
                         if droneData[j] > droneData[highScore] then
                            highScore = j
                         end
                      end
                   end
                   -- swap bees
                   if highScore ~= i then
                      memoryChest.swapStacks(i, highScore)
                      droneData[i], droneData[highScore] = droneData[highScore], droneData[i]
                   end
                end
             end
          end
          logLine("-discarding excess")
          for i = maxMem, maxMem - (maxMem / 10) do
             if droneData[i] ~= nil then
                memoryChest.pushItem(junkDirection,i)
                droneData[i] = nil
             end
          end
       else
          sleep(10)
       end
       log(".")
    end
    log("*")
    logLine()
 end
 
 function scoreBee(droneID)
    local beeDataDrone = getBeeData(droneID)
    local beeDataPrincess = getBeeData(princessSlot)
    local droneSpecies = {getPrimarySpecies(droneID), getSecondarySpecies(droneID)}
    -- check for untargeted species
    if not bees[droneSpecies[1]].targeted or not bees[droneSpecies[2]].targeted then
       return 0
    end
    local princessSpecies = {getPrimarySpecies(princessSlot), getSecondarySpecies(princessSlot)}
    local score
    local maxScore = 0
    for _, combo in ipairs({{princessSpecies[1], droneSpecies[1]}
       ,{princessSpecies[1], droneSpecies[2]}
       ,{princessSpecies[2], droneSpecies[1]}
    ,{princessSpecies[2], droneSpecies[2]}}) do
       -- find maximum score for each combo
       score = (bees[combo[1]].score + bees[combo[2]].score) / 2
       for name, beeData in pairs(bees) do
          if beeData.targeted then
             for i, parents in ipairs(beeData.mutateFrom) do
                if combo[1] == parents[1] and combo[2] == parents[2]
                   or combo[2] == parents[1] and combo[1] == parents[2] then
                   score = (score + beeData.score) / 2
                end
             end
          end
       end
       maxScore = maxScore + score
    end
    -- add one for each combination that results in the maximum score
    score = maxScore
    -- score attributes
    score = score + math.max(scoresFertility[beeDataDrone["active"]["fertility"]], scoresFertility[beeDataPrincess["active"]["fertility"]])
    score = score + math.min(scoresSpeed[tostring(beeDataDrone["active"]["speed"])], scoresSpeed[tostring(beeDataPrincess["active"]["speed"])])
    if beeDataDrone["active"]["nocturnal"] or beeDataPrincess["active"]["nocturnal"] then score = score + scoresAttrib["nocturnal"] end
    if beeDataDrone["active"]["tolerantFlyer"] or beeDataPrincess["active"]["tolerantFlyer"] then score = score + scoresAttrib["tolerantFlyer"] end
    if beeDataDrone["active"]["caveDwelling"] or beeDataPrincess["active"]["caveDwelling"] then score = score + scoresAttrib["caveDwelling"] end
    score = score + math.max(scoresTolerance[string.upper(beeDataDrone["active"]["temperatureTolerance"])], scoresTolerance[string.upper(beeDataPrincess["active"]["temperatureTolerance"])])
    score = score + math.max(scoresTolerance[string.upper(beeDataDrone["active"]["humidityTolerance"])], scoresTolerance[string.upper(beeDataPrincess["active"]["humidityTolerance"])])
    return score
 end
 
 function printHeader()
    logLine()
    logLine("sl t species f spd n f c tmp hmd score ")
    logLine("--|-|-------|-|---|-|-|-|---|---|------")
 end
 
 -- string constants for console output
 toleranceString = {
    ["NONE"] = "  - ",
    ["UP 1"] = " +1 ",
    ["UP 2"] = " +2 ",
    ["UP 3"] = " +3 ",
    ["UP 4"] = " +4 ",
    ["UP 5"] = " +5 ",
    ["DOWN 1"] = " -1 ",
    ["DOWN 2"] = " -2 ",
    ["DOWN 3"] = " -3 ",
    ["DOWN 4"] = " -4 ",
    ["DOWN 5"] = " -5 ",
    ["BOTH 1"] = "+-1 ",
    ["BOTH 2"] = "+-2 ",
    ["BOTH 3"] = "+-3 ",
    ["BOTH 4"] = "+-4 ",
    ["BOTH 5"] = "+-5 "
 }
 
 speedString = {
    ["0.3"] = "0.3", -- Slowest
    ["0.6"] = "0.6", -- Slower
    ["0.8"] = "0.8", -- Slow
    ["1"]   = "1.0", -- Normal
    ["1.2"] = "1.2", -- Fast
    ["1.4"] = "1.4", -- Faster
    ["1.7"] = "1.7"  -- Fastest
 }
 
 function printBee(i)
    local beeData = getBeeData(i)
    log(i < 10 and " "..i.." " or i.." ")
    -- type
    log(string.find(memoryChest.getStackInSlot(i)["rawName"], "princess") and "P " or "D ")
    -- species
    log(getPrimarySpecies(i):gsub("bees%.species%.",""):sub(1,3)..":"..getSecondarySpecies(i):gsub("bees%.species%.",""):sub(1,3).." ")
    -- fertility
    log(tostring(beeData["active"]["fertility"]).." ")
    -- speed
    log(speedString[tostring(beeData["active"]["speed"])].." ")
    -- nocturnal
    log(beeData["active"]["nocturnal"] and "X " or "- ")
    -- flyer
    log(beeData["active"]["tolerantFlyer"] and "X " or "- ")
    -- cave dwelling
    log(beeData["active"]["caveDwelling"] and "X " or "- ")
    -- temperature tolerance
    log(toleranceString[string.upper(beeData["active"]["temperatureTolerance"])])
    -- humidity tolerance
    log(toleranceString[string.upper(beeData["active"]["humidityTolerance"])])
    -- score
    log(droneData[i] and string.format("%5.1d", droneData[i]).." " or "      ")
    logLine()
 end
 
 function dropExcess()
    logLine("dropping excess...")
    for i = ( maxMem - 9 ), maxMem do
       -- drop drones over ( max inv - 9 ) to clear space for newly bred bees and product
       memoryChest.pushItem(junkDirection,i)
    end
 end
 
 function isPurebred(droneID)
    -- check if princess and drone are exactly the same and no chance for mutation
    local princessPrimary = getPrimarySpecies(princessSlot)
    if princessPrimary ~= getSecondarySpecies(princessSlot) then
       return false
    end
    if getPrimarySpecies(droneID) ~= princessPrimary then
       return false
    end
    if getSecondarySpecies(droneID) ~= princessPrimary then
       return false
    end
    local droneBeeData = getBeeData(droneID)
    local princessBeeData = getBeeData(princessSlot)
    for i,key in pairs({ "fertility", "speed", "nocturnal", "tolerantFlyer", "caveDwelling", "temperatureTolerance", "humidityTolerance" }) do
       if
          droneBeeData["active"][key] ~= princessBeeData["active"][key] or
          droneBeeData["inactive"][key] ~= princessBeeData["inactive"][key]
       then
          return false
       end
    end
-   for i, target in ipairs(tArgs) do
+
-      targetBee(target)
+
-      for name, data in pairs(bees) do
+
-         if data.targeted and data.score > 1 then
+
-            logLine(name .. string.rep(" ", 20-#name), data.score)
+
 -- set species and all parents to targeted
 function targetBee(name)
    local bee = bees[name]
    if bee and not bee.targeted then
       bee.targeted = true
       for i, parents in ipairs(bee.mutateFrom) do
          for j, parent in ipairs(parents) do
             targetBee(parent)
          end
       end
    end
 end
 
 tArgs = { ... }
 
 if fs.exists("bee.data") and #tArgs == 0 then
    local recoveredData = fs.open("bee.data", "r")
    local historyData = recoveredData.readLine()
    if historyData then
       historyData = JSON:decode(historyData)
       tArgs[1] = historyData["target"]
       if historyData["count"] ~= nil then
          tArgs[2] = historyData["count"]
       end
       logLine("Recovered old data.")
    end
    recoveredData.close()
 end
 
 
-      droneTarget = analyzeBees()
+
    local myProgramName
-         if isPurebred(droneTarget) then
+
       if type(fileName) == "string" then
          if fileName ~= "" then
             local tempFile = fs.open(fileName,"r")
             if string.sub(tempFile.readLine(),4,6) == "*-*" then
                myProgramName = fileName
                break
             end
          end
       end
    end
    return myProgramName
 end
 
 
 -- set bee graph entry to targeted if species was specified on the command line
 -- otherwise set all entries to targeted
 
 local totalDrones
 local alwaysBreed
 
 if #tArgs > 0 then
    logLine("targeting bee species:")
    fs.delete("bee.data")
    recoveredData = fs.open("bee.data", "w")
    local tempArray = {}
    tempArray["target"] = tArgs[1]
    if tArgs[2] ~= nil then
       tempArray["count"] = math.min(math.max(tonumber(tArgs[2]),1),64)
       totalDrones = math.max(tonumber(tArgs[2]),1)
    end
    recoveredData.write( JSON:encode( tempArray ) )
    recoveredData.close()
    if type(tArgs[1]) == "string" then
       print(string.lower(tArgs[1]))
       while true do
          if tArgs[1]:gsub("^.", string.upper) == "Breedprincess" then
             analyzeBees()
             targetBee(getPrimarySpecies(princessSlot))
             break
          end
          if tArgs[1]:gsub("^.", string.upper) == "Breeddrone" then
             analyzeBees()
             targetBee(getPrimarySpecies(1))
             break
          end
          if true then
             targetBee(tArgs[1]:gsub("^.", string.upper))
             break
          end
          break
       end
    else
       print("You must enter a valid target mutation")
    end
    for name, data in pairs(bees) do
       if data.targeted and data.score > 1 then
          logLine(name .. string.rep(" ", 20-#name), data.score)
       end
    end
    local myProgramName = findMe()
    logLine("Found program:"..myProgramName)
    if myProgramName ~= nil then
       fs.delete("startup")
       local startupFile = fs.open("startup","w")
       startupFile.write("shell.run(\""..myProgramName.."\")")
       startupFile.close()
    else
       logLine("Cannot find program name, you edited the first line of the program didn't you!")
    end
 else
    for _, beeData in pairs(bees) do
       beeData.targeted = true
    end
 end
 
 -- breeding loop ---------------------------------------------------------------
 
 
 
 logLine("Clearing system...")
 clearSystem()
 if not memoryChest.getAllStacks() then
    print("No bees to work on, add bees and restart")
 else
    redstone.setOutput("bottom", true)
    while true do
       analyzeBees()
       droneTarget = sortBees()
       if princessSlot ~= 0 then
          if isPurebred(droneTarget) and memoryChest.getStackInSlot(droneTarget)["qty"] == totalDrone then
             logLine("Bees are purebred.")
             logLine("Princess: "..princessSlot)
             logLine("Drone: "..droneTarget)
             redstone.setOutput("bottom", false)
             fs.delete("bee.data")
             fs.delete("startup")
             break
          end
          memoryChest.pushItemIntoSlot(alvearyDirection,princessSlot,1,1)
          memoryChest.pushItemIntoSlot(alvearyDirection,droneTarget,1,2)
          dropExcess()
       end
       getBees()
    end
 end
 logFile.close()