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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 {}))
;; call plushy->push-internal with possibly-preprocessed plushy
([plushy argmap]
(plushy->push-internal (if (or (> (or (:bmx (:variation argmap)) 0) 0) ;; must strip :gene
(> (or (:bmx-umad (:variation argmap)) 0) 0)) ;; must strip :gene
(filter (complement #{:gene}) plushy)
(plushy->push-internal (if (or (> (or (:bmx (:variation argmap)) 0) 0) ;; must strip :gap
(> (or (:bmx-umad (:variation argmap)) 0) 0)) ;; must strip :gap
(filter (complement #{:gap}) plushy)
plushy)
argmap)))

2
src/propeller/gp.cljc
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@ -184,7 +184,7 @@
n (:bmx-enrichment args)]
(if (or (and prob-bmx (> prob-bmx 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)))]
(gp-loop (-> argmap
(adjust-for-bmx)))))

8
src/propeller/utils.cljc
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@ -165,13 +165,13 @@
(defn count-genes
"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]
(inc (count (filter #(= % :gene) plushy))))
(inc (count (filter #(= % :gap) plushy))))
(defn extract-genes
"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]
(loop [genes []
current-gene []
@ -179,7 +179,7 @@
(cond (empty? remainder)
(conj genes current-gene)
;
(= (first remainder) :gene)
(= (first remainder) :gap)
(recur (conj genes current-gene)
[]
(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]
(let [a-genes (utils/extract-genes plushy-a)
b-genes (utils/extract-genes plushy-b)]
(flatten (interpose :gene
(flatten (interpose :gap
(mapv (fn [g]
(if (< (rand) rate)
(apply min-key #(metrics/levenshtein-distance g %) b-genes)