removed files

1 files changed, 0 insertions, 190 deletions

diff --git a/src/nbc/tabulate.ml b/src/nbc/tabulate.ml
deleted file mode 100644
index dbfbe43..0000000
--- a/src/nbc/tabulate.ml
+++ /dev/null
@@ -1,190 +0,0 @@
-let (|>) a b = b a
-let car, cdr = fst, snd
-let odd n = n land 1 = 1
-let even n = not (odd n)
-module ExtArray = ExtArray.Array
-module ExtList = ExtList.List
-module ExtString = ExtString.String
-module Program = struct
-	let name = "Naive Bayes Classifier - Tabulate"
-	let version = "1.0"
-end
-let chop_extra s = ExtString.strip ~chars:"_- " s
-let any_alphanumeric s =
-	let e = String.length s in
-	let rec loop i =
-		if i = e then false
-		else match s.[i] with
-			'a'..'z' | 'A'..'Z' | '0'..'9' -> true
-			| _ -> loop (i + 1)
-	in loop 0
-let guess_prefix filenames =
-	let s =
-		List.map Misc.basename_without_extension filenames
-			|> Misc.longest_common_substring |> chop_extra
-	in
-	if any_alphanumeric s then s
-	else ""
-module Options = struct
-	let parser = OptParse.OptParser.make ~version:Program.version ()
-	let genomes =
-		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
-		OptParse.OptParser.add parser ~short_name:'g' ~long_name:"genome-list" option;
-		(fun () -> match OptParse.Opt.opt option with
-			Some x -> x
-			| None ->
-				OptParse.OptParser.usage parser ();
-				exit 1
-		)
-	let columns =
-		let option = OptParse.StdOpt.int_option ~default:200 () in
-		OptParse.OptParser.add parser ~short_name:'c' ~long_name:"columns" option;
-		(fun () -> OptParse.Opt.get option)
-	let template =
-		let option = OptParse.StdOpt.str_option ~metavar:"template"
-			~default:"$prefix-$n.csv.gz" () in
-		OptParse.OptParser.add parser ~short_name:'t' ~long_name:"output-template" option;
-		(fun () -> OptParse.Opt.get option)
-	let given_prefix =
-		let x = ref None in
-		OptParse.StdOpt.str_callback ~metavar:"prefix" (fun s -> x := Some s)
-			|> OptParse.OptParser.add parser ~short_name:'p'
-				~long_name:"output-prefix";
-		(fun () -> !x)
-	let files = OptParse.OptParser.parse_argv parser
-	let prefix = match given_prefix () with
-		None -> (
-			match guess_prefix files with
-				"" -> "table"
-				| s -> s
-		) | Some x -> x
-	let string_of_int n = Printf.sprintf "%08u" n
-	let output n = template () |> Misc.substitute ["prefix", prefix; "n", string_of_int n]
-end
-
-exception Collide of string * string * string
-let match_files_to_genomes genomes files =
-	let g = Array.of_list genomes in
-	let gl = Array.length g in
-	let gi = Array.init gl (fun i -> i) in
-	Array.sort (fun ai bi -> compare (String.length g.(bi)) (String.length g.(ai))) gi;
-	let gf = Array.make gl None in
-	List.iter (fun file ->
-		try (
-			let i = ExtArray.find (fun i -> ExtString.exists file g.(i)) gi in
-			match gf.(i) with
-				None -> gf.(i) <- Some file
-				| Some other_file -> raise (Collide (g.(i), other_file, file))
-		) with Not_found -> () (* file does not match any genomes *)
-	) files;
-	let r = ref [] in
-	for i = gl - 1 downto 0 do
-		match gf.(i) with
-			None -> () (* no file matches a given genome *)
-			| Some file -> r := (g.(i), file) :: !r
-	done;
-	!r
-
-let columns = Options.columns ()
-let genomes, files =
-	let genomes = Misc.io_of_file (Options.genomes ()) |> Misc.enum_of_lines
-		|> ExtList.of_enum in
-	let g, f = match_files_to_genomes genomes Options.files |> List.split in
-	Array.of_list g,
-	f |> List.map (fun x -> x, x |> open_in |> IO.input_channel) |> Array.of_list
-
-let newfile, newline, cell, finish = 
-	let i = ref 0 in
-	let open_file () =
-		i := !i + 1;
-		let filename = Options.output !i in
-		Gzip.open_out filename
-	in
-	let c = ref None in
-	let force_out () =
-		match !c with
-			None ->
-				let d = open_file () in
-				c := Some d;
-				d
-			| Some d -> d
-	in
-	let start_of_line = ref true in
-	(* newfile *) (fun () ->
-		(match !c with
-			Some c -> Gzip.close_out c
-			| None -> ());
-		i := !i + 1;
-		c := None
-	),
-	(* newline *) (fun () ->
-		let c = force_out () in
-		Gzip.output_char c '\n';
-		start_of_line := true
-	),
-	(* cell *) (fun s ->
-		let c = force_out () in
-		if not !start_of_line then Gzip.output_char c ',';
-		Gzip.output c s 0 (String.length s);
-		start_of_line := false
-	),
-	(* finish *) (fun () ->
-		match !c with
-			Some c -> Gzip.close_out c
-			| None -> ()
-	)
-
-let read_two_fields (filename, c) =
-		let line = IO.read_line c in
-		match Misc.split2 line with
-			Some x -> x
-			| None ->
-				Printf.eprintf "\
-					There is something wrong with the file %s. \
-					The offending line is:\n%s\n" filename line;
-				exit 1
-
-let output_file () =
-	newfile ();
-	let yes_we_have_input =
-		let x = ref false in
-		(fun () ->
-			if !x then ()
-			else (
-				cell "names";
-				x := true
-			)
-		)
-	in
-	let a = Array.make columns "" in
-	let rec loop i =
-		if i < columns then (
-			try (
-				let name, datum = read_two_fields files.(0) in
-				yes_we_have_input ();
-				cell name;
-				a.(i) <- datum;
-				loop (i + 1)
-			) with IO.No_more_input ->
-				if i > 0 then Array.sub a 0 i
-				else raise End_of_file
-		) else a
-	in
-	let a = loop 0 in
-	let these_columns = Array.length a in
-	newline ();
-	cell genomes.(0);
-	for i = 0 to these_columns - 1 do cell a.(i) done;
-	newline ();
-	for i = 1 to Array.length genomes - 1 do
-		cell genomes.(i);
-		for j = 0 to these_columns - 1 do
-			let _, datum = read_two_fields files.(i) in
-			cell datum
-		done;
-		newline ()
-	done
-
-let () =
-	try while true do output_file () done
-	with End_of_file -> finish ()