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; Copyright (c) Rich Hickey and contributors.
; All rights reserved.
; The use and distribution terms for this software are covered by the
; Eclipse Public License 1.0 (
; which can be found in the file epl-v10.html at the root of this distribution.
; By using this software in any fashion, you are agreeing to be bound by
; the terms of this license.
; You must not remove this notice, or any other, from this software.
; Alioth benchmarks:
(ns alioth.regexdna
(:import [ FileDescriptor FileInputStream])
(:import [java.nio ByteBuffer])
(:import [java.nio.channels FileChannel])
(:import [java.util.regex Pattern])
(set! *warn-on-reflection* true)
(set! *unchecked-math* true)
(def ^:const comment-pattern ">.*\n|\n")
(def ^:const replace-pattern (Pattern/compile "[BDHKMNRSVWY]"))
(def replacements {"B" "(c|g|t)"
"D" "(a|g|t)"
"H" "(a|c|t)"
"K" "(g|t)"
"M" "(a|c)"
"N" "(a|c|g|t)"
"R" "(a|g)"
"S", "(c|g)"
"V", "(a|c|g)"
"W", "(a|t)"
"Y", "(c|t)"})
(def variants ["agggtaaa|tttaccct"
(defn count-occurrences [content regex]
[regex (-> regex Pattern/compile (re-seq content) count)])
(defn replace-codes ^CharSequence [^String content]
(let [buf (StringBuffer.)
m (.matcher replace-pattern content)]
(loop []
(when (.find m)
(.appendReplacement m buf "")
(.append buf (get replacements (.group m)))
(.appendTail m buf)
(defn regexdna [^bytes ba]
(let [input (String. ba "US-ASCII")
content (.replaceAll input comment-pattern "")
replaced (future (replace-codes content))]
(doseq [[regex match-count] (pmap #(count-occurrences content %) variants)]
(println regex match-count))
(doseq [c (map count [input content @replaced])]
(println c))))
(defn -main [& args]
(let [cin (-> FileDescriptor/in FileInputStream. .getChannel)
bb (-> cin .size int ByteBuffer/allocate)]
(.read cin bb)
(regexdna (.array bb)))
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