From b632667ce57af89691407bb8668e1512775278ae Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Fri, 15 Mar 2013 15:26:20 -0400
Subject: nbc added

---
 src/nbc/gene.sml | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 src/nbc/gene.sml

(limited to 'src/nbc/gene.sml')

diff --git a/src/nbc/gene.sml b/src/nbc/gene.sml
new file mode 100644
index 0000000..738e3fe
--- /dev/null
+++ b/src/nbc/gene.sml
@@ -0,0 +1,49 @@
+signature GENE = sig
+	val reverse: string -> string
+	val first: int -> string
+	val next: string -> string option
+end
+
+structure Gene :> GENE = struct
+	fun reverse s =
+		let
+			val n = size s
+			val m = n - 1
+			fun opposite c = case c of
+				#"A" => #"T"
+				| #"T" => #"A"
+				| #"C" => #"G"
+				| #"G" => #"C"
+				| _ => c
+		in
+			CharVector.tabulate (n, fn i => opposite (String.sub (s, m - i)))
+		end
+	fun first order = CharVector.tabulate (order, fn _ => #"A")
+	fun next nmer =
+		let
+			val order = size nmer
+			fun finish (rightmostNonT, replacement) = CharVector.tabulate (
+				order
+				, fn index =>
+					case
+						Int.compare (
+							index
+							, rightmostNonT
+						)
+					of
+						LESS => String.sub (nmer, index)
+						| EQUAL => replacement
+						| GREATER => #"A"
+			)
+			fun continue index =
+				if index < 0 then NONE
+				else case String.sub (nmer, index) of
+					#"A" => SOME (finish (index, #"C"))
+					| #"C" => SOME (finish (index, #"G"))
+					| #"G" => SOME (finish (index, #"T"))
+					| #"T" => continue (index - 1)
+					| _ => raise Fail "Invalid base"
+		in
+			continue (size nmer - 1)
+		end
+end
-- 
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