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/tfxm.ml.html
Source file tfxm.ml
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267
open CFStream type ('input, 'output) t = { name: string option; next: unit -> [ `output of 'output | `end_of_stream | `not_ready ]; feed: 'input -> unit; stop: unit -> unit; } let make_general ?name ~next ~feed ~stop () = {name; next; feed; stop } exception Feeding_stopped_transform of string let feed t i = t.feed i let next t = t.next () let stop t = t.stop () let name t = t.name let make ?name ~feed ~next () = let stopped = ref false in make_general ?name () ~feed:(fun x -> if not !stopped then feed x else raise (Feeding_stopped_transform Option.(value ~default:"" name))) ~next:(fun () -> next !stopped) ~stop:(fun () -> stopped := true) let make_result ?name ~feed ~next () = let stopped = ref false in let one_error_has_occured = ref false in make_general ?name () ~feed:(fun x -> if not !stopped then feed x else raise (Feeding_stopped_transform Option.(value ~default:"" name))) ~next:(fun () -> if !one_error_has_occured then `end_of_stream else begin match next !stopped with | `output (Error _) as e -> one_error_has_occured := true; e | other -> other end) ~stop:(fun () -> stopped := true) let of_function ?name f = let q = Queue.create () in make ?name ~feed:(Queue.enqueue q) () ~next:(fun stopped -> match Queue.dequeue q with | Some o -> `output (f o) | None -> if stopped then `end_of_stream else `not_ready) let identity ?name () = of_function ?name Fun.id let to_stream_fun tr en = let rec loop_until_ready tr en = match next tr with | `output o -> Some o | `end_of_stream -> None | `not_ready -> begin match Stream.next en with | None -> stop tr; loop_until_ready tr en | Some s -> feed tr s; loop_until_ready tr en end in Stream.from (fun _ -> loop_until_ready tr en) let in_channel_strings_to_stream ?(buffer_size=65536) ic tr = to_stream_fun tr (Stream.strings_of_channel ~buffer_size ic) let stream_to_out_channel xs tr oc = Stream.iter (to_stream_fun tr xs) ~f:(Out_channel.output_string oc) let on_input t ~f = { t with feed = fun x -> t.feed (f x) } let on_output t ~f = { t with next = fun () -> match t.next () with | `output o -> `output (f o) | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream } let compose ta tb = let name = sprintf "(compose <%s> <%s>)" Option.(value ~default:"" (name ta)) Option.(value ~default:"" (name tb)) in make_general ~name () ~feed:(fun i -> feed ta i) ~stop:(fun () -> stop ta) ~next:(fun () -> let call_tb_next () = begin match next tb with | `output o -> `output o | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream end in match next ta with | `output o -> feed tb o; call_tb_next () | `not_ready -> call_tb_next () | `end_of_stream -> stop tb; call_tb_next ()) let mix ta tb = let a_buffer = ref None in let name = sprintf "(mix <%s> <%s>)" Option.(value ~default:"" (name ta)) Option.(value ~default:"" (name tb)) in make_general ~name () ~feed:(fun (a, b) -> feed ta a; feed tb b) ~stop:(fun () -> stop ta; stop tb) ~next:(fun () -> begin match !a_buffer with | None -> begin match next ta with | `output oa -> begin match next tb with | `output ob -> `output (`both (oa, ob)) | `not_ready -> a_buffer := Some oa; `not_ready | `end_of_stream -> `end_of_stream end | `not_ready -> `not_ready | `end_of_stream -> begin match next tb with | `output ob -> `output (`right ob) | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream end end | Some oa -> begin match next tb with | `output ob -> a_buffer := None; `output (`both (oa, ob)) | `not_ready -> `not_ready | `end_of_stream -> a_buffer := None; `output (`left oa) end end) let filter_compose left right ~destruct ~reconstruct = let name = sprintf "(part-compose <%s> <%s>)" Option.(value ~default:"" (name left)) Option.(value ~default:"" (name right)) in make_general ~name () ~feed:(fun i -> feed left i) ~stop:(fun () -> stop left) ~next:(fun () -> let call_right_next () = begin match next right with | `output o -> `output (reconstruct (`transformed o)) | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream end in match next left with | `output o -> begin match destruct o with | `transform y -> feed right y; call_right_next () | `bypass n -> `output (reconstruct (`bypassed n)) end | `not_ready -> call_right_next () | `end_of_stream -> stop right; call_right_next ()) let split_and_merge ta tb ~split ~merge = let name = sprintf "(merge <%s> <%s>)" Option.(value ~default:"" (name ta)) Option.(value ~default:"" (name tb)) in make_general ~name () ~feed:(fun z -> match split z with | `left a -> feed ta a | `right b -> feed tb b) ~stop:(fun () -> stop ta; stop tb) ~next:(fun () -> match next ta with | `output o -> `output (merge (`left o)) | `not_ready | `end_of_stream -> begin match next tb with | `output o -> `output (merge (`right o)) | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream end) let on_ok tr ~f = on_output tr ~f:(function | Ok o -> Ok (f o) | Error e -> Error e) let on_error tr ~f = on_output tr ~f:(function | Ok o -> Ok o | Error e -> Error (f e)) let compose_results ~on_error ta tb = let name = sprintf "(compose_results <%s> <%s>)" Option.(value ~default:"" (name ta)) Option.(value ~default:"" (name tb)) in make_general ~name () ~feed:(fun i -> feed ta i) ~stop:(fun () -> stop ta) ~next:(fun () -> let call_tb_next () = begin match next tb with | `output (Ok o) -> `output (Ok o) | `output (Error o) -> `output (Error (on_error (`right o))) | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream end in match next ta with | `output (Ok o) -> feed tb o; call_tb_next () | `output (Error o) -> `output (Error (on_error (`left o))) | `not_ready -> call_tb_next () | `end_of_stream -> stop tb; call_tb_next ()) let compose_results_merge_error ta tb = compose_results ta tb ~on_error:(function `left e -> `left e | `right e -> `right e) let compose_result_left ta tb = let name = sprintf "(compose_result_left <%s> <%s>)" Option.(value ~default:"" (name ta)) Option.(value ~default:"" (name tb)) in make_general ~name () ~feed:(fun i -> feed ta i) ~stop:(fun () -> stop ta) ~next:(fun () -> let call_tb_next () = begin match next tb with | `output o -> `output (Ok o) | `not_ready -> `not_ready | `end_of_stream -> `end_of_stream end in match next ta with | `output (Ok o) -> feed tb o; call_tb_next () | `output (Error o) -> `output (Error o) | `not_ready -> call_tb_next () | `end_of_stream -> stop tb; call_tb_next ()) class type ['input, 'output] object_t = object method next: [ `output of 'output | `end_of_stream | `not_ready ] method feed: 'input -> unit method stop: unit end let to_object tr = object method next = next tr method feed s = feed tr s method stop = stop tr end let of_object o = make_general ~name:(sprintf "of_object_%d" (Oo.id o)) ~next:(fun () -> o#next) ~feed:(fun s -> o#feed s) ~stop:(fun () -> o#stop) ()
sectionYPositions = computeSectionYPositions($el), 10)"
x-init="setTimeout(() => sectionYPositions = computeSectionYPositions($el), 10)"
>