--- a/rosalind.asd Mon Nov 05 19:49:03 2018 -0500
+++ b/rosalind.asd Wed Nov 07 20:38:33 2018 -0500
@@ -43,5 +43,6 @@
(:file "grph")
(:file "prtm")
(:file "mrna")
- (:file "splc")))))))
+ (:file "splc")
+ (:file "lcsm")))))))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/problems/lcsm.lisp Wed Nov 07 20:38:33 2018 -0500
@@ -0,0 +1,79 @@
+(in-package :rosalind)
+
+;; This one sucked. We should use suffix trees some day but I just hacked this
+;; together for now.
+
+(defparameter *input-lcsm* ">Rosalind_1
+GATTACA
+>Rosalind_2
+TAGACCA
+>Rosalind_3
+ATACA")
+
+(defun compute-substring-table% (string1 string2)
+ ;; Compute the table of substring lengths.
+ ;;
+ ;; a b c d e c
+ ;; x 0 0 0 0 0 0
+ ;; a 1 0 0 0 0 0
+ ;; b 0 2 0 0 0 0
+ ;; c 0 0 3 0 0 1
+ ;; e 0 0 0 0 0 1
+ (check-type string1 string)
+ (check-type string2 string)
+ (let ((table (make-array (list (length string1) (length string2)))))
+ (dotimes (i1 (length string1))
+ (dotimes (i2 (length string2))
+ (setf (aref table i1 i2)
+ (if (char= (aref string1 i1) (aref string2 i2))
+ (if (or (zerop i1) (zerop i2))
+ 1
+ (1+ (aref table (1- i1) (1- i2))))
+ 0))))
+ table))
+
+(defun-inline substring-at% (string index length)
+ ;; Given a matching string/table-index and a length, return the substring.
+ ;; The table effectively stores (start, end] but subseq wants [start, end).
+ (let ((end (1+ index)))
+ (subseq string (- end length) end)))
+
+(defun-inline find-substrings-of-length% (table string1 length)
+ ;; Find all the substrings in the table with the given length.
+ (iterate (for (l i1 nil) :in-array table)
+ (when (= length l)
+ (collect (substring-at% string1 i1 length)))))
+
+(defun-inline find-maximum-length% (table)
+ ;; Find the highest length in the table.
+ (iterate (for l :across-flat-array table)
+ (maximizing l)))
+
+(defun longest-common-substrings (string1 string2)
+ "Return a list of the longest common substrings of `string1` and `string2`."
+ (let ((table (compute-substring-table% string1 string2)))
+ (find-substrings-of-length% table string1 (find-maximum-length% table))))
+
+(defun longest (strings)
+ "Return a list of the longest strings in `strings`."
+ (remove-if-not
+ (curry #'= (alexandria:extremum (mapcar #'length strings) #'>))
+ strings :key #'length))
+
+(defun longest-common-substrings-of-any (substrings string)
+ "Return the longest common substrings of `string` and any one of `substrings`."
+ (-<> (iterate
+ (for substring :in substrings)
+ (appending (longest-common-substrings substring string)))
+ longest
+ (remove-duplicates <> :test #'string=)))
+
+(define-problem lcsm (data stream)
+ *input-lcsm*
+ "AC"
+ (let ((lines (iterate (for (nil line) :in-fasta data)
+ (collect line))))
+ (-<> (reduce #'longest-common-substrings-of-any (rest lines)
+ :initial-value (list (first lines)))
+ (sort <> #'string<) ; tests
+ first)))
--- a/src/utils.lisp Mon Nov 05 19:49:03 2018 -0500
+++ b/src/utils.lisp Wed Nov 07 20:38:33 2018 -0500
@@ -228,7 +228,7 @@
;;;; Testing ------------------------------------------------------------------
(defmacro define-test (problem input output &optional (test 'string=))
`(test ,(symb 'test- problem)
- (is (,test ,output (,problem ,input)))))
+ (is (,test ,output (aesthetic-string (,problem ,input))))))
(defun run-tests ()
(1am:run))
@@ -246,7 +246,7 @@
(setf ,arg ,(ecase type
(string `(ensure-string ,arg))
(stream `(ensure-stream ,arg))))
- (aesthetic-string (progn ,@body)))
+ (progn ,@body))
(setf (get ',symbol 'rosalind-name) ,(string-downcase name))
(define-test ,symbol ,sample-input ,sample-output)
',symbol))))
@@ -256,7 +256,7 @@
(defun solve% (problem)
(with-open-file (input (problem-data-path problem))
- (pbcopy (funcall problem input))))
+ (pbcopy (aesthetic-string (funcall problem input)))))
(defmacro solve (name)
`(solve% ',(symb 'problem- name)))