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Rename :gene to :gap

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This commit is contained in:
Lee Spector 2023-12-02 23:02:07 -05:00
parent 30a87a2688
commit a0bd993281
4 changed files with 9 additions and 9 deletions
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6
src/propeller/genome.cljc
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@ -48,8 +48,8 @@ They hold the genetic material for an `individual`. In the initial population, w
(plushy->push plushy {})) (plushy->push plushy {}))
;; call plushy->push-internal with possibly-preprocessed plushy ;; call plushy->push-internal with possibly-preprocessed plushy
([plushy argmap] ([plushy argmap]
(plushy->push-internal (if (or (> (or (:bmx (:variation argmap)) 0) 0) ;; must strip :gene (plushy->push-internal (if (or (> (or (:bmx (:variation argmap)) 0) 0) ;; must strip :gap
(> (or (:bmx-umad (:variation argmap)) 0) 0)) ;; must strip :gene (> (or (:bmx-umad (:variation argmap)) 0) 0)) ;; must strip :gap
(filter (complement #{:gene}) plushy) (filter (complement #{:gap}) plushy)
plushy) plushy)
argmap))) argmap)))

2
src/propeller/gp.cljc
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@ -184,7 +184,7 @@
n (:bmx-enrichment args)] n (:bmx-enrichment args)]
(if (or (and prob-bmx (> prob-bmx 0)) (if (or (and prob-bmx (> prob-bmx 0))
(and prob-bmx-umad (> prob-bmx-umad 0))) (and prob-bmx-umad (> prob-bmx-umad 0)))
(update args :instructions concat (repeat (or n 1) :gene)) (update args :instructions concat (repeat (or n 1) :gap))
args)))] args)))]
(gp-loop (-> argmap (gp-loop (-> argmap
(adjust-for-bmx))))) (adjust-for-bmx)))))

8
src/propeller/utils.cljc
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@ -165,13 +165,13 @@
(defn count-genes (defn count-genes
"A utility for best match crossover (bmx). Returns the number of segments "A utility for best match crossover (bmx). Returns the number of segments
between (and before and after) instances of :gene." between (and before and after) instances of :gap."
[plushy] [plushy]
(inc (count (filter #(= % :gene) plushy)))) (inc (count (filter #(= % :gap) plushy))))
(defn extract-genes (defn extract-genes
"A utility for best match crossover (bmx). Returns the segments of the plushy "A utility for best match crossover (bmx). Returns the segments of the plushy
before/between/after instances of :gene." before/between/after instances of :gap."
[plushy] [plushy]
(loop [genes [] (loop [genes []
current-gene [] current-gene []
@ -179,7 +179,7 @@
(cond (empty? remainder) (cond (empty? remainder)
(conj genes current-gene) (conj genes current-gene)
; ;
(= (first remainder) :gene) (= (first remainder) :gap)
(recur (conj genes current-gene) (recur (conj genes current-gene)
[] []
(rest remainder)) (rest remainder))

2
src/propeller/variation.cljc
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@ -139,7 +139,7 @@ The function `new-individual` returns a new individual produced by selection and
[plushy-a plushy-b rate] [plushy-a plushy-b rate]
(let [a-genes (utils/extract-genes plushy-a) (let [a-genes (utils/extract-genes plushy-a)
b-genes (utils/extract-genes plushy-b)] b-genes (utils/extract-genes plushy-b)]
(flatten (interpose :gene (flatten (interpose :gap
(mapv (fn [g] (mapv (fn [g]
(if (< (rand) rate) (if (< (rand) rate)
(apply min-key #(metrics/levenshtein-distance g %) b-genes) (apply min-key #(metrics/levenshtein-distance g %) b-genes)