From 9066ea884129957fe899d6d10cba1e17547214b9 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 13 Nov 2013 13:07:23 -0500
Subject: remove nbc:

---
 src/nbc/probabilities-by-read.sml | 210 --------------------------------------
 1 file changed, 210 deletions(-)
 delete mode 100644 src/nbc/probabilities-by-read.sml

(limited to 'src/nbc/probabilities-by-read.sml')

diff --git a/src/nbc/probabilities-by-read.sml b/src/nbc/probabilities-by-read.sml
deleted file mode 100644
index acd8041..0000000
--- a/src/nbc/probabilities-by-read.sml
+++ /dev/null
@@ -1,210 +0,0 @@
-local
-	fun usage result = (
-		TextIO.output (
-			TextIO.stdErr
-			, CommandLine.name ()
-		^ " <order> <input FASTA> <file of nmers to count>\n"
-		); OS.Process.exit result
-	)
-in
-	val (order, input, toCount) = case CommandLine.arguments () of
-		[order, input, toCount] => (case Int.fromString order of
-			NONE => usage OS.Process.failure
-			| SOME order => (order, input, toCount)
-		) | ["--help"] => usage OS.Process.success
-		| _ => usage OS.Process.failure
-end
-
-datatype result = Success | Failure
-fun warn message = TextIO.output (
-	TextIO.stdErr
-	, (
-		"warning: "
-		^ message
-		^ "\n"
-	)
-)
-
-signature NMER_TABLE = sig
-	type nmer
-	type table
-
-	(*
-		Create the table. Only the provided nmers will be counted.
-	*)
-	val create: nmer list -> table
-
-	(*
-		Increment the count for a given nmer. If the nmer was
-		not provided at table creation, do nothing.
-	*)
-	val bump: table * nmer -> unit
-
-	(*
-		Reset all counts to zero. Do not change the list of
-		nmers to count.
-	*)
-	val clear: table -> unit
-
-	(*
-		Apply a function to all nmers and their counts, in
-		lexicographic order.
-	*)
-	val app: (nmer * int -> unit) -> table -> unit
-end
-
-functor NmerTable (Nmer: NMER)
-:> NMER_TABLE where type nmer = Nmer.nmer
-= struct
-	structure HashTable = HashTableFn (
-		type hash_key = Nmer.nmer
-		val hashVal = Nmer.hash
-		val sameKey = Nmer.equal
-	)
-	exception NotFound
-	type nmer = Nmer.nmer
-	type table = {
-		indexes: int HashTable.hash_table
-		, counts: int array
-		, nmers: nmer vector
-	}
-	fun create list =
-		let
-			val indexes = HashTable.mkTable (1024, NotFound)
-			val nmers =
-				let
-					val array = Array.fromList list
-				in
-					ArrayQSort.sort Nmer.compare array
-					; Array.vector array
-				end
-		in
-			Vector.appi (fn (index, nmer) =>
-				HashTable.insert indexes (nmer, index)
-			) nmers
-			; {
-				indexes = indexes
-				, nmers = nmers
-				, counts = Array.array (
-					Vector.length nmers
-					, 0
-				)
-			}
-		end
-	fun bump ({indexes, nmers = _, counts}, nmer) =
-		case HashTable.find indexes nmer of
-			NONE => ()
-			| SOME index => Array.update (
-				counts
-				, index
-				, Array.sub (counts, index) + 1
-			)
-	fun clear {indexes = _, nmers = _, counts} =
-		Array.modify (fn _ => 0) counts
-	fun app execute {indexes = _, nmers, counts} =
-		Vector.appi (fn (index, nmer) =>
-			execute (nmer, Array.sub (counts, index))
-		) nmers
-end
-
-functor Input (
-	structure Nmer: NMER
-	structure NmerTable: NMER_TABLE
-	sharing type Nmer.nmer = NmerTable.nmer
-) = SingleSidedFasta (
-	structure Nmer = Nmer
-	structure File = struct
-		type argument = NmerTable.table
-		type file = argument
-		type read = Int64.int ref
-		type nmer = Nmer.nmer
-		datatype result = datatype result
-		exception NotFound
-		fun startFile table = table
-		fun startRead (table, _) = ref (0: Int64.int)
-		fun nmer (table, (total: Int64.int ref), nmer) = (
-			total := !total + 1
-			; NmerTable.bump (table, nmer)
-		)
-		fun put string = TextIO.output (TextIO.stdOut, string)
-		fun stopRead (table, total) =
-			let
-				val realFromInt64 =
-					Real.fromLargeInt o Int64.toLarge
-				val realTotal = realFromInt64 (!total)
-				val toString = Real.fmt (
-					StringCvt.FIX (SOME 17)
-				)
-				fun probability count = real count / realTotal
-				infix |>
-				fun argument |> function = function argument
-				val first = ref true
-			in
-				NmerTable.app (fn (nmer, count) => (
-					if !first then first := false
-					else put "\t"
-					; count
-						|> probability
-						|> toString
-						|> put
-				)) table
-				; put "\n"
-				; NmerTable.clear table
-				; total := 0
-			end
-		fun stopFile _ = Success
-		fun invalidFormat _ = Failure
-	end
-)
-
-structure Nmer = Nmer (
-	val order = order
-	structure Word = Word64
-)
-structure NmerTable = NmerTable (Nmer)
-structure Input = Input (
-	structure Nmer = Nmer
-	structure NmerTable = NmerTable
-)
-
-val table =
-	let
-		fun build collect goose = case collect goose of
-			NONE => nil
-			| SOME egg =>
-				egg :: build collect goose
-		fun chopEnd string = String.extract (
-			string
-			, 0
-			, SOME (size string - (
-				if String.isSuffix "\r\n" string
-				then 2
-				else 1
-			))
-		)
-		val line = Option.map chopEnd o TextIO.inputLine
-		val lines = build line
-		val instream = TextIO.openIn toCount
-		fun fromStringWithWarning string =
-			case Nmer.fromString string of
-				NONE => (
-					warn (
-						string
-						^ " is not a valid nmer"
-					); NONE
-				) | someNmer => someNmer
-		val nmers = List.mapPartial
-			fromStringWithWarning
-			(lines instream)
-	in
-		TextIO.closeIn instream
-		; NmerTable.create nmers
-	end
-
-val () = case Input.process (table, TextIO.openIn input) of
-	Failure => (
-		TextIO.output (
-			TextIO.stdErr
-			, "input is not valid FASTA\n"
-		); OS.Process.exit OS.Process.failure
-	) | Success => ()
-- 
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