6aa19c08b5cf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/problems/cat.lisp	Sat Apr 30 21:06:41 2022 -0400
@@ -0,0 +1,49 @@
+(defpackage :rosalind/cat (:use :cl :rosalind :losh :iterate))
+(in-package :rosalind/cat)
+
+(defparameter *input*
+  ">Rosalind_57
+AUAU")
+
+(defparameter *output*
+  "2")
+
+
+;;;; Problem ------------------------------------------------------------------
+(defun rna-bases-pair-p (base1 base2)
+  (char= base1 (ecase base2
+                 (#\A #\U)
+                 (#\U #\A)
+                 (#\G #\C)
+                 (#\C #\G))))
+
+(defun rna-matches (rna &aux (cache (make-hash-table)))
+  (recursively ((start 0)
+                (end (length rna)))
+    (if (= start end)
+      1
+      (alexandria:ensure-gethash (complex start end) cache
+        (iterate
+          ;; Arbitrarily pick char 0 as one of the ends of the match to avoid
+          ;; needing to cross the end of the RNA sequence when recurring.
+          (with b1 = (char rna start))
+          ;; Check each matching base, but count by 2 to avoid odd-length
+          ;; subsequences when recurring.
+          (for b2 :in-string rna :from (1+ start) :below end :by 2 :with-index i)
+          (when (rna-bases-pair-p b1 b2)
+            (summing (* (recur (1+ start) i)
+                        (recur (1+ i) end)))))))))
+
+(define-problem cat (data stream) *input* *output*
+  (mod (rna-matches (nth-value 1 (u:read-fasta data))) 1000000))
+
+
+#; Scratch --------------------------------------------------------------------
+
+
+(problem-cat)
+
+(problem-cat "UAGCGUGAUCAC")
+
+(time (solve cat))
+