removed files

1 files changed, 0 insertions, 98 deletions

diff --git a/src/nbc/main.sml b/src/nbc/main.sml
deleted file mode 100644
index 361d9ca..0000000
--- a/src/nbc/main.sml
+++ /dev/null
@@ -1,98 +0,0 @@
-structure Main = struct
-
-fun |> (x, f) = f x
-infix |>
-
-val order = Options.order
-val genomes = case Options.genomes of
-	SOME x => x |> TextIO.openIn |> Misc.sequenceLines
-	| NONE => Options.genomesDir |> Misc.sortedDirectoryNoPrefix |> Sequence.fromList
-fun input () =
-	case Fasta.sequence (Gzip.openIn Options.input) of
-		NONE => Fail.fail "input file is not FASTA format"
-		| SOME x =>
-			Sequence.map (fn (header, data) =>
-				(header, String.map Char.toUpper data)
-			) x
-fun output genome =
-	let
-		fun inner format = case format of
-			Options.Matlab {variable, file} =>
-				let
-					val matlab = Matlab.openOut file
-					val doubleArray = Matlab.beginDoubleArray (matlab, variable)
-				in {
-					write = fn (_, score) =>
-						Matlab.writeDouble (doubleArray, score)
-					, close = fn () => (
-						Matlab.concludeDoubleArray doubleArray
-						; Matlab.closeOut matlab
-					)
-				} end
-			| Options.Text filename =>
-				let
-					val gzip = Gzip.openOut filename
-				in {
-					write = fn (header, score) =>
-						TextIO.output (
-							gzip
-							, Real.fmt (StringCvt.FIX (SOME 8)) score
-						)
-					, close = fn () => TextIO.closeOut gzip
-				} end
-			| Options.Dual {text, matlab} =>
-				let
-					val text = inner (Options.Text text)
-					val matlab = inner (Options.Matlab matlab)
-				in {
-					write = fn x => (
-						#write text x
-						; #write matlab x
-					), close = fn () => (
-						#close text ()
-						; #close matlab ()
-					)
-				} end
-	in
-		inner (Options.output genome)
-	end
-fun totalWords (genome, order) =
-        let
-		val name = Options.totalWords (genome, order)
-		val input = TextIO.openIn name
-	in
-		(case Option.mapPartial Real.fromString (Misc.inputLine input) of
-			NONE => Fail.fail ("could not read number from " ^ name)
-			| SOME r => r
-		) before TextIO.closeIn input
-	end
-
-val () =
-	Sequence.app (fn gname =>
-		let
-			val {write, close} = output gname
-			val totalWords = totalWords (gname, order)
-			val genome = (
-				Stopwatch.start ("Loading genome " ^ gname)
-				; Genome.load (gname, order)
-				before Stopwatch.finish ()
-			)
-		in
-			Stopwatch.start ("Scoring fragments")
-			; input () |> Sequence.app (fn (header, fragment) =>
-				write (
-					header
-					, Score.score (
-						order
-						, Options.missConstant
-						, fn nmer => Genome.get (genome, nmer)
-						, totalWords
-						, fragment
-					)
-				)
-			); Stopwatch.finish ()
-			; close ()
-		end
-	) genomes
-
-end