Added sequence generation option by giving a generator method

project.clj

@@ -1,4 +1,4 @@
-(defproject nature "1.0.0"
+(defproject org.clojars.btezergil/nature "1.0.0"
             :description "A simple genetic algorithms library for Clojure(Script)"
             :url "https://github.com/nnichols/nature"
             :license {:name "Eclipse Public License"

src/nature/core.cljc

@@ -3,6 +3,19 @@
             [nature.population-operators :as po]
             [nature.monitors :as monitors]))
 
+(defn evolution-loop
+  "Evolution loop that is used commonly by sequence generator function and random generation from allele set."
+  [initial-population generations population-size binary-operators unary-operators options]
+  (let [solutions (max 1 (:solutions options))
+        carry-over (max 1 (:carry-over options))
+        monitors (:monitors options)]
+    (loop [population initial-population 
+           current-generation 0]
+      (when monitors (monitors/apply-monitors monitors population current-generation))
+      (if (>= current-generation generations)
+        (take solutions (sort-by :fitness-score #(> %1 %2) population))
+        (recur (po/advance-generation population population-size binary-operators unary-operators {:carry-over carry-over}) (inc current-generation))))))
+
 (defn evolve
   "Create and evolve a population under the specified conditions until a termination criteria is reached
   `allele-set` is a collection of legal genome values
@@ -13,23 +26,28 @@
   `binary-operators` is a collection of partial functions accepting and returning 1 or more individuals
   `unary-operators` is a collection of partial functions accepting and returning exactly 1 individual
   `options` an optional map of pre-specified keywords to values that further tune the behavior of nature.
-      Current examples follow:
-      `:carry-over` an integer representing the top n individuals to be carried over between each generation. Default is 1
-      `:solutions` an integer representing the top n individuals to return after evolution completes. Default is 1
-      `:monitors` a sequence of functions, assumed to be side-effectful, to be executed against `population` and `current-genration` for run-time stats. Default is nil"
+  Current examples follow:
+  `:carry-over` an integer representing the top n individuals to be carried over between each generation. Default is 1
+  `:solutions` an integer representing the top n individuals to return after evolution completes. Default is 1
+  `:monitors` a sequence of functions, assumed to be side-effectful, to be executed against `population` and `current-genration` for run-time stats. Default is nil"
   ([allele-set genome-length population-size generations fitness-function binary-operators unary-operators]
    (evolve allele-set genome-length population-size generations fitness-function binary-operators unary-operators {:solutions 1, :carry-over 1}))
 
   ([allele-set genome-length population-size generations fitness-function binary-operators unary-operators options] ;; TODO - Curry the genetic operators one more level, so the fitness-function can be pressed in
    {:pre [(and (every? coll? [allele-set binary-operators unary-operators])
                (every? int? [genome-length population-size generations])
                (fn? fitness-function))]}
-   (let [solutions (max 1 (:solutions options))
-         carry-over (max 1 (:carry-over options))
-         monitors (:monitors options)]
-     (loop [population (io/build-population population-size allele-set genome-length fitness-function)
-            current-generation 0]
-       (when monitors (monitors/apply-monitors monitors population current-generation))
-       (if (>= current-generation generations)
-         (take solutions (sort-by :fitness-score #(> %1 %2) population))
-         (recur (po/advance-generation population population-size binary-operators unary-operators {:carry-over carry-over}) (inc current-generation)))))))
+   (evolution-loop (io/build-population population-size allele-set genome-length fitness-function) population-size generations binary-operators unary-operators options)))
+
+(defn evolve-with-sequence-generator
+  "Same with evolve method, but takes a sequence generator function instead of an allele set and genome length.
+  This method uses the sequence generator function to generate sequences for the initial population."
+  ([generator-function population-size generations fitness-function binary-operators unary-operators]
+   (evolve-with-sequence-generator generator-function population-size generations fitness-function binary-operators unary-operators {:solutions 1, :carry-over 1}))
+
+  ([generator-function population-size generations fitness-function binary-operators unary-operators options]
+   {:pre [(and (every? coll? [binary-operators unary-operators])
+               (every? int? [population-size generations])
+               (every? fn? [generator-function fitness-function]))]}
+   (evolution-loop (io/build-population population-size generator-function fitness-function) population-size generations binary-operators unary-operators options)))
+

src/nature/initialization_operators.cljc

@@ -32,6 +32,10 @@
           :fitness-score (fitness-function genetic-sequence))))
 
 (defn build-population
-  "Build `population-size` individuals by invoking `build-individual` on random, conforming genetic sequences."
-  [population-size alleles sequence-length fitness-function]
-  (repeatedly population-size #(build-individual (generate-sequence alleles sequence-length) fitness-function)))
+  "Build `population-size` individuals by invoking `build-individual` on random, conforming genetic sequences.
+  If given a sequence generator function, uses this function to generate valid sequences instead."
+  ([population-size sequence-generator-function fitness-function]
+   (repeatedly population-size #(build-individual (sequence-generator-function) fitness-function)))
+
+  ([population-size alleles sequence-length fitness-function]
+   (repeatedly population-size #(build-individual (generate-sequence alleles sequence-length) fitness-function))))