package biocaml
The OCaml Bioinformatics Library
Install
Dune Dependency
Authors
Maintainers
Sources
biocaml-0.11.2.tbz
sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d
sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6
doc/src/biocaml.unix/lines.ml.html
Source file lines.ml
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open CFStream type item = Line.t [@@deriving sexp] module MakeIO (Future : Future.S) = struct open Future let read r = Reader.lines r |> Pipe.map ~f:Line.of_string_unsafe let write w pipe_r = Pipe.iter pipe_r ~f:(fun item -> Writer.write_line w (item : item :> string) ) let write_file ?perm ?append file pipe_r = Writer.with_file ?perm ?append file ~f:(fun w -> write w pipe_r) end include MakeIO(Future_unix) let of_char_stream cstr = let f _ = match Stream.peek cstr with | None -> None | Some _ -> let ans = Buffer.create 100 in let rec loop () = match Stream.next cstr with | Some c -> if Char.(c <> '\n') then (Buffer.add_char ans c; loop()) | None -> () in loop(); Some (Buffer.contents ans |> Line.of_string_unsafe) in Stream.from f let of_channel cin = let f _ = In_channel.input_line cin |> Option.map ~f:Line.of_string_unsafe in Stream.from f let of_string s = let n = String.length s in let f pos = if pos >= n then None else if Char.equal s.[pos] '\n' then Some (Line.of_string_unsafe "", pos + 1) else let sub, new_pos = match String.lfindi ~pos s ~f:Char.(fun _ c -> c = '\n') with | Some pos' -> String.sub s ~pos ~len:(pos' - pos), pos' + 1 | None -> String.suffix s (n - pos), n in Some (Line.of_string_unsafe sub, new_pos) in Stream.unfold 0 ~f let to_channel xs oc = Stream.iter xs ~f:(fun l -> Out_channel.output_string oc (l : item :> string); Out_channel.newline oc ) let with_file fn ~f = In_channel.with_file fn ~f:(fun ic -> f (read ic) ) module Buffer = struct type t = { mutable unfinished_line : string option; lines : item Queue.t; mutable parsed_lines : int; filename : string option; } let make ?filename () = {unfinished_line = None; lines = Queue.create (); parsed_lines = 0; filename} let feed_line p s = Queue.enqueue p.lines s let feed_string p s = let lines = String.split s ~on:'\n' in let rec faux = function | [] -> assert false | [ "" ] -> (* last char was a "\n" *) () | [ s ] -> (* there is a partial line at the end *) p.unfinished_line <- Some s; | h :: t -> Queue.enqueue p.lines (Line.of_string_unsafe h); faux t in match p.unfinished_line, lines with | _, [] -> assert false | _, [""] -> () | None, l -> faux l | Some s, h :: t -> p.unfinished_line <- None; faux ((s ^ h) :: t) let queued_lines p = Queue.length p.lines let peek_line p = Queue.peek p.lines let next_line p = let l = Queue.dequeue p.lines in if Poly.(l <> None) then ( p.parsed_lines <- p.parsed_lines + 1; ); l exception No_next_line let next_line_exn p = match next_line p with | Some s -> s | None -> raise No_next_line let current_position p = Pos.make ?source:p.filename ~line:p.parsed_lines () let is_empty p = Queue.is_empty p.lines && Poly.(p.unfinished_line = None) let contents p = Queue.to_list p.lines, p.unfinished_line let empty p = (Queue.clear p.lines; p.unfinished_line <- None) end module Transform = struct let string_to_item () = let buf = Buffer.make () in Tfxm.make ~name:"string_to_lines" ~feed:(Buffer.feed_string buf) ~next:(function | true -> (match Buffer.next_line buf with | Some line -> `output line | None -> (match Buffer.contents buf with | [], None -> `end_of_stream | [], Some unfinished_line -> (Buffer.empty buf; `output (Line.of_string_unsafe unfinished_line)) | _ -> assert false ) ) | false -> (match Buffer.next_line buf with | None -> `not_ready | Some line -> `output line ) ) () let item_to_string ?(buffer:[`clear of int | `reset of int]= `reset 1024) () = let module Buffer = Caml.Buffer in let buffer, clear_buffer = match buffer with | `clear s -> (Buffer.create s, Buffer.clear) | `reset s -> (Buffer.create s, Buffer.reset) in Tfxm.make ~name:"lines_to_string" () ~feed:(fun l -> Buffer.add_string buffer (l : Line.t :> string); Buffer.add_char buffer '\n') ~next:(fun stopped -> match Buffer.contents buffer with | "" -> if stopped then `end_of_stream else `not_ready | s -> clear_buffer buffer; `output s) let group2 () = let queue : (item * item) Queue.t= Queue.create () in let item1 = ref None in Tfxm.make ~name:"group2" ~feed:(function item -> match !item1 with | Some item1' -> ( Queue.enqueue queue (item1', item); item1 := None ) | None -> item1 := Some item ) ~next:(fun stopped -> match Queue.dequeue queue with | Some ij -> `output (Ok ij) | None -> if not stopped then `not_ready else (match !item1 with | None -> `end_of_stream | Some _ -> `output (Error `premature_end_of_input) ) ) () let make ?name ?filename ~next ~on_error () = let lo_parser = Buffer.make ?filename () in Tfxm.make ?name () ~feed:(Buffer.feed_string lo_parser) ~next:(fun stopped -> match next lo_parser with | `output (Ok r) -> `output (Ok r) | `output (Error r) -> `output (Error (on_error (`next r))) | `not_ready -> if stopped then ( if Buffer.is_empty lo_parser then `end_of_stream else let l,o = Buffer.contents lo_parser in `output (Error (on_error (`incomplete_input (Buffer.current_position lo_parser, (l :> string list), o)))) ) else `not_ready) let make_merge_error = make ~on_error:(function | `next e -> e | `incomplete_input e -> `incomplete_input e) end
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