src/problems/cat.lisp @ 0c68769a8788

(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))