package biotk
Bioinformatics toolkit
Install
Dune Dependency
Authors
Maintainers
Sources
biotk-v0.0.0.tbz
sha256=4d487ddb8951d51f0c461a42da2e7f4a8fedcc3691718a93ac577da5d3058b2e
sha512=491ccccba2edb4565946361bbf3a0e764b57238cc8ee8af469a717dcdf18711cf9516becc91956997b870c8944ebe6d1662a2edbb5567c439991c5afd3bceb15
doc/src/biotk.pipes/pipe.ml.html
Source file pipe.ml
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type void module type Monad = sig type 'a t val return : 'a -> 'a t val bind : 'a t -> ('a -> 'b t) -> 'b t end module type S = sig type 'a monad type 'a thunk = unit -> 'a type finalizer = (unit -> unit monad) option type ('i, 'o, 'r) t = | Has_output of 'o * ('i, 'o, 'r) t thunk * finalizer | Needs_input of ('i option -> ('i, 'o, 'r) t) | Done of 'r | PipeM of ('i, 'o, 'r) t monad thunk type 'a source = (void, 'a, unit) t type 'a sink = ('a, void, unit) t val return : 'r -> (_, _, 'r) t val bind : ('i, 'o, 'a) t -> ('a -> ('i, 'o, 'b) t) -> ('i, 'o, 'b) t module Monad_infix : sig val ( >>= ) : ('i, 'o, 'a) t -> ('a -> ('i, 'o, 'b) t) -> ('i, 'o, 'b) t end val await : unit -> ('a, _, 'a option) t val yield : 'o -> (_, 'o, unit) t val compose : ('i, 'a, _) t -> ('a, 'o, 'r) t -> ('i, 'o, 'r) t val ( $$ ) : ('i, 'a, _) t -> ('a, 'o, 'r) t -> ('i, 'o, 'r) t val run : (void, void, 'r) t -> 'r monad val bracket : (unit -> 'a monad) -> ('a -> unit monad) -> ('a -> ('i, 'o, 'r) t) -> ('i, 'o, 'r) t val fold : 'r -> ('i -> 'r -> 'r) -> ('i, void, 'r) t val map : ('i -> 'o) -> ('i, 'o, unit) t val mapi : (int -> 'i -> 'o) -> ('i, 'o, unit) t val filter : ('i -> bool) -> ('i, 'i, unit) t val filter_map : ('i -> 'o option) -> ('i, 'o, unit) t val from_list : 'a list -> 'a source val to_list : unit -> ('a, void, 'a list) t val all : unit -> (('a, 'b) result, void, ('a list, 'b) result) t val loop : ('a -> 'b option -> 'a * 'c list) -> 'a -> ('b, 'c, unit) t val loop' : ('a -> 'b option -> ('a * 'c list, 'd) result) -> 'a -> ('b, 'c, (unit, 'd) result) t val drop : int -> ('a, 'a, unit) t end module Make(M : Monad) = struct let ( >>= ) x f = M.bind x f type 'a monad = 'a M.t type 'a thunk = unit -> 'a type finalizer = (unit -> unit M.t) option type ('i, 'o, 'r) t = | Has_output of 'o * ('i, 'o, 'r) t thunk * finalizer | Needs_input of ('i option -> ('i, 'o, 'r) t) | Done of 'r | PipeM of ('i, 'o, 'r) t M.t thunk type 'a source = (void, 'a, unit) t type 'a sink = ('a, void, unit) t let return x = Done x let rec bind (* : ('i, 'o, 'a) t -> ('a -> ('i, 'o, 'b) t) -> ('i, 'o, 'b) t *) = fun x f -> match x with | Has_output (o, next, cleanup) -> Has_output (o, (fun () -> bind (next ()) f), cleanup) | Needs_input on_input -> Needs_input (fun i -> bind (on_input i) f) | Done r -> f r | PipeM m -> PipeM (fun () -> m () >>= fun p -> M.return (bind p f) ) module Monad_infix = struct let ( >>= ) x f = bind x f end let await () = Needs_input (fun i -> Done i) let yield x = Has_output (x, (fun () -> Done ()), None) let finalizer_compose f g = match f, g with | None, None -> None | Some f, None -> Some f | None, Some g -> Some g | Some f, Some g -> Some (fun () -> f () >>= g) let finalize = function | None -> M.return () | Some f -> f () let compose p q = let rec go_right final left = function | Has_output (o, next, clean) -> let next () = go_right final left (next ()) in let clean = finalizer_compose clean final in Has_output (o, next, clean) | Needs_input f -> go_left f final left | Done r -> PipeM (fun () -> finalize final >>= fun () -> M.return (Done r) ) | PipeM m -> PipeM (fun () -> m () >>= fun p -> M.return ( go_right final left p ) ) and go_left next_right final = function | Has_output (o, next, final') -> go_right final' (next ()) (next_right (Some o)) | Needs_input f -> Needs_input (fun i -> go_left next_right final (f i)) | Done r -> go_right None (Done r) (next_right None) | PipeM m -> PipeM (fun () -> m () >>= fun p -> M.return (go_left next_right final p) ) in go_right None p q let ( $$ ) = compose let rec run = function | Done r -> M.return r | PipeM m -> m () >>= run | Has_output _ -> assert false | Needs_input _ -> assert false let bracket alloc free f = let rec add_clean_up f = function | Done x -> PipeM (fun () -> f () >>= fun () -> M.return (Done x) ) | Has_output (o, next, final) -> Has_output (o, (fun () -> add_clean_up f (next ())), finalizer_compose (Some f) final) | Needs_input next -> Needs_input (fun i -> add_clean_up f (next i)) | PipeM m -> PipeM (fun () -> m () >>= fun next -> M.return (add_clean_up f next) ) in PipeM (fun () -> alloc () >>= fun seed -> M.return (add_clean_up (fun () -> free seed) (f seed)) ) let rec fold init f = Needs_input (function | None -> Done init | Some i -> fold (f i init) f ) let rec map f = let open Monad_infix in await () >>= function | None -> return () | Some x -> yield (f x) >>= fun () -> map f let mapi f = let open Monad_infix in let rec aux i = await () >>= function | None -> return () | Some x -> yield (f i x) >>= fun () -> aux (i + 1) in aux 0 let rec filter f = let open Monad_infix in await () >>= function | None -> return () | Some x -> if f x then yield x >>= fun () -> filter f else filter f let rec filter_map f = let open Monad_infix in await () >>= function | None -> return () | Some x -> match f x with | None -> filter_map f | Some y -> yield y >>= fun () -> filter_map f let from_list l = let open Monad_infix in let rec loop = function | [] -> Done () | h :: t -> yield h >>= fun () -> loop t in loop l let to_list () = let open Monad_infix in let rec loop accu = await () >>= function | None -> Done (List.rev accu) | Some x -> loop (x :: accu) in loop [] let all () = let open Monad_infix in let rec loop accu = await () >>= function | None -> Done (Ok (List.rev accu)) | Some (Ok x) -> loop (x :: accu) | Some (Error _ as e) -> Done e in loop [] let rec loop f st = let open Monad_infix in await () >>= fun i -> let (st', ys) = f st i in let rec loop' ys = match ys, i with | [], None -> Done () | [], Some _ -> loop f st' | h :: t, _ -> yield h >>= fun () -> loop' t in loop' ys let rec loop' f st = let open Monad_infix in await () >>= fun i -> match f st i with | Ok (st', ys) -> let rec inner ys = match ys, i with | [], None -> Done (Ok ()) | [], Some _ -> loop' f st' | h :: t, _ -> yield h >>= fun () -> inner t in inner ys | Error _ as e -> Done e let drop n = let open Monad_infix in let rec loop k = await () >>= function | None -> return () | Some x -> if k <= 0 then yield x >>= fun () -> loop 0 else loop (k - 1) in loop n end
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