remove nbc:

1 files changed, 0 insertions, 290 deletions

diff --git a/src/nbc/count.sml b/src/nbc/count.sml
deleted file mode 100644
index d036050..0000000
--- a/src/nbc/count.sml
+++ /dev/null
@@ -1,290 +0,0 @@
-datatype sides = Single | Double
-datatype labeled = Labeled | Unlabeled
-local
-	(*
-	val perWord = ref NONE
-	val total = ref NONE
-	*)
-	val order = ref (SOME 15)
-	val sides = ref Double
-	val labeled = ref Labeled
-	val optionsWithoutHelp = [
-		(* {
-			short = "w", long = ["per-word"]
-			, desc = GetOpt.ReqArg (
-				fn file => perWord := SOME file
-				, "file"
-			), help = "file to store per-word counts in"
-		}, {
-			short = "t", long = ["total"]
-			, desc = GetOpt.ReqArg (
-				fn file => total := SOME file
-				, "file"
-			), help = "file to store total count in"
-		}, *) {
-			short = "r", long = ["order"]
-			, desc = GetOpt.ReqArg (
-				fn size => order := Int.fromString size
-				, "size"
-			), help = "word size"
-		}, {
-			short = "1", long = ["single"]
-			, desc = GetOpt.NoArg (fn () => sides := Single)
-			, help = "only count one side"
-		}, {
-			short = "u", long = ["unlabeled"]
-			, desc = GetOpt.NoArg (fn () => labeled := Unlabeled)
-			, help = "emit counts for every possible nmer, without labels"
-		}
-	]
-	fun usageString () = GetOpt.usageInfo {
-		header = CommandLine.name () ^ " <options> <input FASTA file> ..."
-		, options = optionsWithoutHelp
-	} ^ "\n"
-	datatype status = Success | Failure
-	fun displayHelpAndExit status = (
-		TextIO.output (
-			TextIO.stdErr
-			, usageString ()
-		); OS.Process.exit (case status of
-			Success => OS.Process.success
-			| Failure => OS.Process.failure
-		)
-	)
-	val options = {
-		short = "h", long = ["help"]
-		, desc = GetOpt.NoArg (fn () => displayHelpAndExit Success)
-		, help = "display help"
-	} :: optionsWithoutHelp
-in
-	val (_, files) = GetOpt.getOpt {
-		argOrder = GetOpt.Permute
-		, options = options
-		, errFn = fn errorMessage => (
-			TextIO.output (TextIO.stdErr, errorMessage ^ "\n")
-			; displayHelpAndExit Failure
-		)
-	} (CommandLine.arguments ())
-	(*
-	val perWordFileName = case !perWord of
-		NONE => (
-			TextIO.output (
-				stdErr
-				, "per-word file name required but not provided\n"
-			); displayHelpAndExit Failure
-		) | SOME fileName => fileName
-	val totalFileName = case !total of
-		NONE => (
-			TextIO.output (
-				stdErr
-				, "total file name required but not provided\n"
-			); displayHelpAndExit Failure
-		) | SOME fileName => fileName
-	*)
-	val order = case !order of
-		NONE => (
-			TextIO.output (
-				TextIO.stdErr
-				, "invalid order\n"
-			); displayHelpAndExit Failure
-		) | SOME integer => integer
-	val sides = !sides
-	val labeled = !labeled
-end
-
-signature COLLECTION = sig
-	type collection
-	type nmer
-	val empty: unit -> collection
-	val add: collection * nmer -> unit
-	val get: collection * nmer -> int
-	val app: (nmer * int -> unit) -> collection -> unit
-end
-
-functor Collection (Nmer: NMER)
-:> COLLECTION where type nmer = Nmer.nmer = struct
-	type nmer = Nmer.nmer
-	structure Table = HashTableFn (
-		type hash_key = nmer
-		val hashVal = Nmer.hash
-		val sameKey = Nmer.equal
-	)
-	type collection = int ref Table.hash_table
-	exception NotFound
-	fun empty () = Table.mkTable (256 * 1024, NotFound)
-	fun add (table, nmer) = case Table.find table nmer of
-		NONE => Table.insert table (nmer, ref 1)
-		| SOME count => count := !count + 1
-	fun get (table, nmer) = case Table.find table nmer of
-		NONE => 0
-		| SOME (ref count) => count
-	fun app execute table = Table.appi (fn (nmer, ref count) =>
-		execute (nmer, count)
-	) table
-end
-
-datatype result = Success | Failure
-
-signature OUTPUT = sig
-	type collection
-	val output: collection -> unit
-end
-
-functor Unlabeled (
-	structure Nmer: NMER
-	structure Collection: COLLECTION
-		sharing type Collection.nmer = Nmer.nmer
-) :> OUTPUT
-	where type collection = Collection.collection
-= struct
-	type collection = Collection.collection
-	fun put string = TextIO.output (TextIO.stdOut, string)
-	fun single count = (
-		put (Int.toString count)
-		; put "\n"
-	)
-	fun output collection =
-		let
-			fun continue nmer = (
-				single (Collection.get (collection, nmer))
-				;
-					if nmer = Nmer.maximum then ()
-					else continue (Nmer.next nmer)
-			)
-		in
-			continue (Nmer.minimum)
-		end
-end
-
-functor Labeled (
-	structure Nmer: NMER
-	structure Collection: COLLECTION
-		sharing type Collection.nmer = Nmer.nmer
-) :> OUTPUT
-	where type collection = Collection.collection
-= struct
-	type collection = Collection.collection
-	fun put string = TextIO.output (TextIO.stdOut, string)
-	fun single (nmer, count) = (
-		put (Nmer.toString nmer)
-		; put " "
-		; put (Int.toString count)
-		; put "\n"
-	)
-	fun output collection = Collection.app single collection
-end
-
-functor File (
-	structure Collection: COLLECTION
-	structure Output: OUTPUT
-		sharing type Collection.collection = Output.collection
-) :> FILE
-	where type nmer = Collection.nmer
-	where type result = result
-	where type argument = unit
-= struct
-	type argument = unit
-	type file = Collection.collection
-	type read = unit
-	type nmer = Collection.nmer
-	type result = result
-	fun startFile _ = Collection.empty ()
-	fun startRead _ = ()
-	fun nmer (counts, (), nmer) = Collection.add (counts, nmer)
-	fun stopRead (_, ()) = ()
-	fun stopFile counts = (
-		Output.output counts
-		; Success
-	)
-	fun invalidFormat file = Failure
-end
-
-functor Everything (Nmer: NMER) = struct
-	structure Collection = Collection (Nmer)
-	structure Unlabeled = File (
-		structure Collection = Collection
-		structure Output = Unlabeled (
-			structure Nmer = Nmer
-			structure Collection = Collection
-		)
-	)
-	structure Labeled = File (
-		structure Collection = Collection
-		structure Output = Labeled (
-			structure Nmer = Nmer
-			structure Collection = Collection
-		)
-	)
-	structure SingleSidedUnlabeled = SingleSidedFasta (
-		structure Nmer = Nmer
-		structure File = Unlabeled
-	)
-	structure DoubleSidedUnlabeled = DoubleSidedFasta (
-		structure Nmer = Nmer
-		structure File = Unlabeled
-	)
-	structure SingleSidedLabeled = SingleSidedFasta (
-		structure Nmer = Nmer
-		structure File = Labeled
-	)
-	structure DoubleSidedLabeled = DoubleSidedFasta (
-		structure Nmer = Nmer
-		structure File = Labeled
-	)
-end
-
-structure Everything32 = Everything (
-	Nmer (
-		val order = order
-		structure Word = Word32
-	)
-)
-structure Everything64 = Everything (
-	Nmer (
-		val order = order
-		structure Word = Word64
-	)
-)
-
-val process =
-	if order <= 32 then (case sides of
-		Single => (case labeled of
-			Unlabeled => Everything32.SingleSidedUnlabeled.process
-			| Labeled => Everything32.SingleSidedLabeled.process
-		) | Double => (case labeled of
-			Unlabeled => Everything32.DoubleSidedUnlabeled.process
-			| Labeled => Everything32.DoubleSidedLabeled.process
-		)
-	) else (case sides of
-		Single => (case labeled of
-			Unlabeled => Everything64.SingleSidedUnlabeled.process
-			| Labeled => Everything64.SingleSidedLabeled.process
-		) | Double => (case labeled of
-			Unlabeled => Everything64.DoubleSidedUnlabeled.process
-			| Labeled => Everything64.DoubleSidedLabeled.process
-		)
-	)
-
-val () =
-	let
-		fun one name =
-			let
-				val instream = TextIO.openIn name
-				val result = process ((), instream)
-			in
-				TextIO.closeIn instream
-				; case result of
-					Success => true
-					| Failure => (
-						TextIO.output (
-							TextIO.stdErr
-							, name
-							^ ": invalid format\n"
-						); false
-					)
-			end
-		fun all names = List.all one names
-	in
-		if all files then ()
-		else OS.Process.exit OS.Process.failure
-	end