;;  ----------   FLIBS'NLOGO   ----------------------------------------------------------------------------------
;;  -------------------------------------------------------------------------------------------------------------



breed   [flibs flib]     ;; FLiBs (finite living blobs) are the agents of the model: they are structured as
                         ;; finite automata (1, 2). They have "a finite number of states; an input signal
                         ;; causes it to change automatically from one state to another.
                         ;; The kind of automaton used in a flib also generates signals. Incoming and outgoing
                         ;; signals are represented within the automaton by symbols. When a signal is received,
                         ;; the automaton changes its state and emits a second signal" (2). A flib is considered
                         ;; perfect predictor i.e. very well adapted when its outgoing signals (previsions)
                         ;; is equal to the next incoming environmental signal. Signals are always binary digits.


flibs-own [chromosome    ;; every flib owns a chromosome that is a string coding its state transition table;
           state         ;; the current state of the flib
           fitness]      ;; a measure of its forestalling ability


globals [counter         ;; a counter useful in different procedures
         new-input       ;; the incoming environmental signal
         average         ;; mean of flibs population performances
         best            ;; the best flibs performance value
         worst           ;; the worst flibs performance value
         donor           ;; one very performing flib sharing part of its genes
         recipient       ;; one flib acquiring genes from a donor
         a-split         ;; a first cut in the recipient's chromosome
         b-split         ;; a second cut in the recipient's chromosome
         wild-type       ;; a natural state chromosome
         optimal]        ;; the flib's chromosome showing a perfect prevision ability



;;  ----------   SETUP PROCEDURES   -----------------------------------------------------------------------------
;;  -------------------------------------------------------------------------------------------------------------

to setup                 ;; initializing the model
  clear-all
  reset-ticks
  set counter 0
  create-flibs num-flibs [
    set shape "face happy"
    set size 1.8
    set chromosome ""
    set label fitness
    fd 2 + random 7]
  ask flibs [chromosome-genesis]
end 

to chromosome-genesis   ;; chromosomes are strings randomly built through an iterative procedure: even string's
                        ;; positions are 0 or 1: they represent a possible outgoing signal; odd string's
                        ;; positions represent possible flib's states determined by NUM-STATES slider
  set chromosome word chromosome (word (random 2) (random num-states))
  set counter counter + 1
  ifelse counter < num-states * 2 [chromosome-genesis]
    [set counter 0]
end 



;;  ----------   RUNTIME PROCEDURES   ---------------------------------------------------------------------------
;;  -------------------------------------------------------------------------------------------------------------

to search
  ;; testing flibs' prevision ability along 100 cycles and results are analyzed
  set counter 0
  ask flibs [set fitness 0 set state 0]
  ask flibs [chrom-test]
  performances-analysis

  ;; a new generation begins
  tick
  ask flibs [move]
  output-print ""
  output-print word "tick: " ticks

  ;; if flibs population harbours a perfect predictor, the goal of the genetic algorithm is reached
  if best = 100 [final-message stop]

  ;; if flibs population doesn't harbour any perfect predictor, genetic algorithm activates two operators:
  ;; genetic shuffling (as a consequence of mating processes) and mutagenesis

  ;; every generation one recombination event occurs by default, this frequency can be
  ;; lowered by the slider "MATE-RATE"
  ifelse random-float 1 < mate-rate [conjugation]
    [output-print "no mating event"]

  ;; every generation, one mutagenesis process occurs  by default, this frequency can be
  ;; lowered by the slider MUTATION-RATE
  ifelse random-float 1 < mutation-rate
    [set wild-type [who] of one-of flibs ask flib wild-type [mutate]]
    [output-print "no mutation event"]
end 

to final-message
  output-print "        EUREKA!!!"
  set optimal [who] of one-of flibs with [fitness = 100]
  ifelse best > 9  [output-type word "id: " optimal] [output-type word "id: 0" optimal]
  output-type word " optimal predictor:         " [chromosome] of flib optimal
  output-print word "     fitness: " [fitness] of flib optimal
  output-print ""
  output-print "--- no genetic variation (look at the previous generation) ---"
  output-print ""
end 

to-report  patches-ahead [ rad dis ] ; reports to turtles a set of patches ahead
  report [ patches in-radius rad ] of patch-ahead dis
end 

to move
   ifelse (any? other turtles-on patches-ahead 1 1)
    [ bk 0.1 lt random-float 360]
    [fd 0.01]
end 


;; Operator 1: FITNESS EVALUATION
;; --------------------------------------------------------------------------------------------------------------

to chrom-test
  ;; an environmental input symbol is read from the given sequence
  set new-input read-from-string item (counter mod (length environmental-cycle)) environmental-cycle
  ;; only 0 or 1 symbols are accepted
  if new-input != 0 and new-input != 1 [
    show "error: invalid environmental value"
    stop]
  ;; each flibs prevision ability is tested and fitness is updated
  if read-from-string  item (4 * state + 2 * new-input) chromosome =
        read-from-string item ((counter + 1) mod (length environmental-cycle)) environmental-cycle
            [set fitness (fitness + 1)]
  ;; new flibs state is computed
  set state read-from-string item (4 * state + 2 * new-input + 1) chromosome
  set counter counter + 1
  ;; the cycle is repeated 100 times
  if counter < 100 [chrom-test]
  set counter 0
end 

to performances-analysis
  ask flibs [
  set average mean [fitness] of flibs
  set best max [fitness] of flibs
  set worst min [fitness] of flibs
  set label fitness
  ;; flibs performances are visually represented through emoticons language
  ifelse fitness < 55
    [set shape "face sad"] [ifelse fitness < 85
    [set shape "face neutral"]
    [set shape "face happy"]]
  ]
end 


;; Operator 2: RECOMBINATION
;; --------------------------------------------------------------------------------------------------------------

to conjugation
  clear-links
  ;; the conjugation process requires two flibs' chromosomes: the donor and the recipient
  ;; just the second one undergoes to recombination
  select-flibs
  ;; a link highlighted the two mating flibs
  ask flib donor [create-link-to flib recipient]
  ask flib recipient [recombination]
end 

to select-flibs
  set donor [who] of one-of flibs with [fitness = best]
  set recipient [who] of one-of flibs
  if donor = recipient [select-flibs]     ;; self conjugation is forbidden
  ;; generating report about the selection process
  ifelse donor > 9  [output-type word "id: " donor] [output-type word "id: 0" donor]
  output-type word " donor chromosome:      " [chromosome] of flib donor
  output-print word "     fitness: " [fitness] of flib donor
  ifelse recipient > 9  [output-type word "id: " recipient]  [output-type word "id: 0" recipient]
  output-type word " recipient chromosome:  " [chromosome] of flib recipient
  output-print word "     fitness: " [fitness] of flib recipient
end 

to recombination
  ;; a gene's sequence included between a-split and b-split restriction sites is randomly chosen
  set a-split random (num-states * 4)
  set b-split random (num-states * 4)
  if a-split = b-split [recombination]
  set counter 0
  hybridization
  ;; generating a report about genetic shuffling
  ifelse recipient > 9  [output-type word "id: " recipient]  [output-type word "id: 0" recipient]
  output-print word " hybridized chromosome: " chromosome
  output-type "- flanking positions of replaced fragment:  [ "
  output-type word a-split " - "
  output-print word b-split " [ "
end 

to hybridization
 ;; the genes' sequence included between a-split and b-split restriction sites on a random
 ;; flib is replaced by the homologous sequence of one of the most performing flibs;
 ;; chromosomes are treated as circle-shaped
 if a-split < b-split [
    set chromosome replace-item (a-split + counter)
    chromosome (item (a-split + counter) [chromosome] of flib donor)
    set counter (counter + 1) if counter < b-split - a-split
    [hybridization]]
 if a-split > b-split [
    set chromosome replace-item ((a-split + counter) mod (num-states * 4))
    chromosome (item ((a-split + counter) mod (num-states * 4)) [chromosome] of flib donor)
    set counter (counter + 1) if counter < (num-states * 4) - (a-split - b-split)
    [hybridization]]
  set counter 0
end 


;; Operator 3: MUTAGENESIS
;; --------------------------------------------------------------------------------------------------------------

to mutate
  ;; managing mutation and generating a report
  ifelse wild-type > 9  [output-type word "id: " wild-type]  [output-type word "id: 0" wild-type]
  output-type word " wild-type chromosome:  " [chromosome] of flib wild-type
  output-print word "     fitness: " [fitness] of flib wild-type
  ;; mutations occur randomly at a given frequency on just one locus
  let dice random length chromosome
  let muton read-from-string item dice chromosome
  ifelse dice mod 2 = 0
    [set chromosome replace-item dice chromosome word ((muton + 1) mod 2) ""]
    [set chromosome replace-item dice chromosome word ((muton + 1) mod num-states) ""]
  ifelse wild-type > 9  [output-type word "id: " wild-type] [output-type word "id: 0" wild-type]
  output-print word " mutant chromosome:     " [chromosome] of flib wild-type
end