From d8402962f11cfc2aaba6a58d94ff0a3456d8d2ac Mon Sep 17 00:00:00 2001
From: Lee Spector <lspector@hampshire.edu>
Date: Tue, 26 Dec 2023 17:27:41 -0500
Subject: [PATCH] Remove rather than filling empty genes.

---
 src/propeller/genome.cljc    |  2 +-
 src/propeller/utils.cljc     | 14 +++++---------
 src/propeller/variation.cljc |  4 ++--
 3 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/src/propeller/genome.cljc b/src/propeller/genome.cljc
index 8d9d98b..e72a48f 100755
--- a/src/propeller/genome.cljc
+++ b/src/propeller/genome.cljc
@@ -12,7 +12,7 @@ They hold the genetic material for an `individual`. In the initial population, w
                            #(utils/random-instruction instructions))]
     (if bmx?
       (-> plushy
-          (utils/fill-empty-genes instructions)
+          (utils/remove-empty-genes)
           (utils/enforce-gene-length-limit bmx-gene-length-limit))
       plushy)))
 
diff --git a/src/propeller/utils.cljc b/src/propeller/utils.cljc
index cce6b62..7be6302 100755
--- a/src/propeller/utils.cljc
+++ b/src/propeller/utils.cljc
@@ -198,17 +198,13 @@
   (+ (* 0.5 (metrics/multiset-distance p1 p2))
      (math/abs (- (count p1) (count p2)))))
 
-(defn fill-empty-genes
+(defn remove-empty-genes
   "A utility function for bmx-related genetic operators. Returns the provided
    plushy with any empty genes (regions before/between/after instances of :gap)
-   filled with a new random instruction."
-  [plushy instructions]
-  (flatten (interpose :gap
-                      (mapv (fn [gene]
-                              (if (empty? gene)
-                                (random-instruction instructions)
-                                gene))
-                            (extract-genes plushy)))))
+   removed."
+  [plushy]
+  (vec (flatten (interpose :gap (filter #(not (empty? %))
+                                        (extract-genes plushy))))))
 
 (defn break-up
   "A utility function for bmx-related genetic operators. Returns the provided
diff --git a/src/propeller/variation.cljc b/src/propeller/variation.cljc
index 1a6da17..ba83d13 100644
--- a/src/propeller/variation.cljc
+++ b/src/propeller/variation.cljc
@@ -244,7 +244,7 @@ The function `new-individual` returns a new individual produced by selection and
          (->  (bmx plushy1 plushy2 bmx-exchange-rate max-distance argmap)
               (uniform-gap-addition gap-change-prob)
               (uniform-gap-deletion gap-change-prob)
-              (utils/fill-empty-genes (:instructions argmap))
+              (utils/remove-empty-genes)
               (utils/enforce-gene-length-limit (:bmx-gene-length-limit argmap))))
        ;
        :umad ;; uniform mutation by addition and deletion, see uniform-deletion for the
@@ -277,7 +277,7 @@ The function `new-individual` returns a new individual produced by selection and
               (uniform-gap-deletion gap-change-prob)
               (uniform-addition (:instructions argmap) umad-rate)
               (uniform-deletion umad-rate)
-              (utils/fill-empty-genes (:instructions argmap))
+              (utils/remove-empty-genes)
               (utils/enforce-gene-length-limit (:bmx-gene-length-limit argmap))))
        ;
        :rumad ;; responsive UMAD, uses a deletion rate computed from the actual