removed files

1 files changed, 0 insertions, 202 deletions

diff --git a/src/nbc/options.sml b/src/nbc/options.sml
deleted file mode 100644
index 907c95a..0000000
--- a/src/nbc/options.sml
+++ /dev/null
@@ -1,202 +0,0 @@
-signature OPTIONS = sig
-	val order: int
-	val input: string
-	val genomesDir: string
-	val genomes: string option
-	val genomeText: int * string -> string
-	val totalWords: string * int -> string
-	val missConstant: real
-	datatype output =
-		Matlab of {variable: string, file: string}
-		| Text of string
-		| Dual of {text: string, matlab: {variable: string, file: string}}
-	val output: string -> output
-	val arguments: string list
-end
-
-structure Options :> OPTIONS = struct
-	fun |> (x, f) = f x
-	infix |>
-	datatype outformat = Otext | Omatlab | Odual
-	local
-		val order = ref 15
-		val fasta = ref NONE
-		val genomesDir = ref "/var/lib/genomes"
-		val genomes = ref NONE
-		val genomeText = ref "$genomes_dir/$genome/${order}perword.gz"
-		val totalWords = ref "$genomes_dir/$genome/${order}total"
-		val missConstant = ref (1.0 / 26067530.0 / 1000000.0)
-		val outFormat = ref Otext
-		val variable = ref "ps_g"
-		val outFile = ref "$input-$order-$genome.$extension"
-		fun withDefault (description, default) = concat (
-			description
-			:: " ("
-			:: (case default of
-				NONE => ["no default)"]
-				| SOME x => ["default: ", x, ")"])
-		)
-		val options = [
-			{
-				short = "r", long = ["order"]
-				, help = withDefault
-					("Set the length of words used in matches", NONE)
-				, desc = GetOpt.ReqArg (
-					fn x => case Int.fromString x of
-						NONE => Fail.fail
-							"given order is not a valid integer"
-						| SOME y => order := y
-					, "integer"
-				)
-			}, {
-				short = "a", long = ["fasta-input"]
-				, help = "FASTA input file"
-				, desc = GetOpt.ReqArg (fn x => fasta := SOME x, "filename")
-			}, {
-				short = "j", long = ["genomes-dir"]
-				, help = withDefault (
-					"Set the directory where genomes are stored"
-					, SOME (!genomesDir)
-				), desc = GetOpt.ReqArg (fn x => genomesDir := x, "directory")
-			}, {
-				short = "g", long = ["genome-list"]
-				, help = withDefault (
-					"Read genomes from this file, one per line"
-					, !genomes
-				), desc = GetOpt.ReqArg (fn x => genomes := SOME x, "filename")
-			}, {
-				short = "w", long = ["genome-text"]
-				, help = withDefault (
-					"Filename to read per-word counts from"
-					, SOME (!genomeText)
-				), desc = GetOpt.ReqArg (fn x => genomeText := x, "filename")
-			}, {
-				short = "t", long = ["total-words"]
-				, help = withDefault (
-					"Filename to read total word counts from"
-					, SOME (!totalWords)
-				), desc = GetOpt.ReqArg (fn x => totalWords := x, "filename")
-			}, {
-				short = "k", long = ["miss-constant"]
-				, help = withDefault (
-					"Set the constant used for scoring missing words"
-					, SOME (Real.toString (!missConstant))
-				), desc = GetOpt.ReqArg (
-					fn x => (case Real.fromString x of 
-						SOME y => missConstant := y
-						| NONE => Fail.fail
-							"given miss constant is not a valid number"
-					), "number"
-				)
-			}, {
-				short = "x", long = ["text"]
-				, help = "Select gzipped text output (default)"
-				, desc = GetOpt.NoArg (fn () => outFormat := Otext)
-			}, {
-				short = "m", long = ["matlab"]
-				, help = "Select Matlab binary output"
-				, desc = GetOpt.NoArg (fn () => outFormat := Omatlab)
-			}, {
-				short = "u", long = ["dual"]
-				, help = "Select both gzipped text and Matlab binary output"
-				, desc = GetOpt.NoArg (fn () => outFormat := Odual)
-			}, {
-				short = "v", long = ["variable"]
-				, help = withDefault (
-					"Set Matlab output variable"
-					, SOME (!variable)
-				), desc = GetOpt.ReqArg (fn x => variable := x, "name")
-			}, {
-				short = "o", long = ["output-file"]
-				, help = withDefault (
-					"Set output filename(s)"
-					, SOME (!outFile)
-				), desc = GetOpt.ReqArg (fn x => outFile := x, "filename")
-			}
-		]
-		val optionsWithHelp = {
-			short = "h", long = ["help"]
-			, help = "Display help"
-			, desc = GetOpt.NoArg (fn () => (
-				print (
-					GetOpt.usageInfo {
-						header = "score <options>"
-						, options = options
-					} ^ "\n"
-				); OS.Process.exit OS.Process.success
-			))
-		} :: options
-	in
-		val (_, arguments) = GetOpt.getOpt {
-			argOrder = GetOpt.Permute
-			, options = optionsWithHelp
-			, errFn = print
-		} (CommandLine.arguments ())
-		val order = !order
-		val input = case !fasta of 
-			NONE => Fail.fail "No input file given"
-			| SOME x => x
-		val genomesDir = !genomesDir
-		val genomes = !genomes
-		val genomeText = fn (order, genome) => (
-			case
-				Misc.substitute [
-					("genomes_dir", genomesDir)
-					, ("genome", genome)
-					, ("order", Int.toString order)
-				] (!genomeText)
-			of
-				NONE => Fail.fail "bad per-word count filename syntax"
-				| SOME x => x
-		)
-		val totalWords = fn (genome, order) => (
-			case
-				Misc.substitute [
-					("genomes_dir", genomesDir)
-					, ("genome", genome)
-					, ("order", Int.toString order)
-				] (!totalWords)
-			of
-				NONE => Fail.fail "bad total word count filename syntax"
-				| SOME x => x
-		)
-		val missConstant = !missConstant
-		datatype output =
-			Matlab of {variable: string, file: string}
-			| Text of string
-			| Dual of {text: string, matlab: {variable: string, file: string}}
-		fun output genome =
-			let
-				val common = [
-					("input", Misc.basenameWithoutExtension input)
-					, ("order", Int.toString order)
-					, ("genome", genome)
-				]
-				fun textName () =
-					case Misc.substitute
-						(("extension", "txt.gz") :: common) (!outFile)
-					of
-						NONE => Fail.fail "bad text output filename syntax"
-						| SOME x => x
-				fun matlabName () =
-					case Misc.substitute
-						(("extension", "mat") :: common) (!outFile)
-					of
-						NONE => Fail.fail "bad Matlab output filename syntax"
-						| SOME x => x
-			in
-				case !outFormat of
-					Otext => Text (textName ())
-					| Omatlab => Matlab {
-						variable = !variable
-						, file = matlabName ()
-					} | Odual => Dual {
-						text = textName ()
-						, matlab = {
-							variable = !variable
-							, file = matlabName ()
-						}
-					}
-			end
-	end
-end