package biotk
Bioinformatics toolkit
Install
Dune Dependency
Authors
Maintainers
Sources
biotk-0.1.0.tbz
sha256=0dfe118d4a2698aec7eb108449a2b63a8c0ebd6dc29809608f75b8fa611dd0a1
sha512=898e0239e6626bb88e00a0080337d8a054d49097be8d2a32b181a5fcf29b925c9bacda5a02ce255a7afd80248eb76a789b80f0e9788906ccff426e5330abef0e
doc/src/biotk.croquis/croquis.ml.html
Source file croquis.ml
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open Gg open Vg open Core_kernel type point = float * float module Float_array = struct let min xs = Array.fold xs ~init:Float.max_value ~f:Float.min let max xs = Array.fold xs ~init:Float.min_value ~f:Float.max end module Scaling = struct type 'a t = 'a -> float let id x = x let linear ~domain:(from_lo, from_hi) ~range:(to_lo, to_hi) = let delta = to_hi -. to_lo in let rho = delta /. (from_hi -. from_lo) in fun x -> (x -. from_lo) *. rho +. to_lo end module Viewport = struct type t = { scale_x : float -> float ; scale_y : float -> float ; } let linear ~xlim ~ylim ~size:(w, h) = { scale_x = Scaling.linear ~domain:xlim ~range:(0., w) ; scale_y = Scaling.linear ~domain:ylim ~range:(0., h) } let make ?(scale_x = Scaling.id) ?(scale_y = Scaling.id) () = { scale_x ; scale_y } let id = { scale_x = ident ; scale_y = ident ; } let scale_x vp = vp.scale_x let scale_y vp = vp.scale_y let scale vp (x, y) = (vp.scale_x x, vp.scale_y y) end type thickness = [ | `normal | `thick ] let thickness_value = function | `thin -> 0.001 | `normal -> 0.01 | `thick -> 0.1 type point_shape = [ | `bullet | `circle ] module Font = struct type t = Vg_text.Font.t Lazy.t let ascender x = Vg_text.Font.ascender (Lazy.force x) let descender x = Vg_text.Font.descender (Lazy.force x) let xmin x = Vg_text.Font.xmin (Lazy.force x) let xmax x = Vg_text.Font.xmax (Lazy.force x) let ymin x = Vg_text.Font.ymin (Lazy.force x) let ymax x = Vg_text.Font.ymax (Lazy.force x) let embedded_load fn = Lazy.from_fun (fun () -> let src = Stdlib.Option.get (Font_data.read fn) in match Vg_text.Font.load_from_string src with | Ok f -> f | Error (#Otfm.error as e) -> let buf = Buffer.create 253 in let fmt = Format.formatter_of_buffer buf in Otfm.pp_error fmt e ; Format.pp_print_flush fmt () ; failwith (Buffer.contents buf) | Error (`Read_error msg) -> failwithf "Read_error: %s" msg () ) let dejavu_sans_mono = embedded_load "DejaVuSansMono.ttf" let dejavu_sans_mono_bold = embedded_load "DejaVuSansMono-Bold.ttf" let dejavu_sans_mono_oblique = embedded_load "DejaVuSansMono-Oblique.ttf" let dejavu_sans_mono_bold_oblique = embedded_load "DejaVuSansMono-BoldOblique.ttf" let liberation_sans = embedded_load "LiberationSans-Regular.ttf" let liberation_sans_bold = embedded_load "LiberationSans-Bold.ttf" let liberation_sans_italic = embedded_load "LiberationSans-Italic.ttf" let liberation_sans_bold_italic = embedded_load "LiberationSans-BoldItalic.ttf" let default = liberation_sans end module Picture = struct class type t = object method render : image method bbox : Box2.t end let points ?(col = Color.black) ?(shape = `bullet) ~x ~y () = let xmin = Float_array.min x in let xmax = Float_array.max x in let ymin = Float_array.min y in let ymax = Float_array.max y in object method render = let area = match shape with | `bullet -> `Anz | `circle -> `O { P.o with P.width = thickness_value `thin } in let mark = I.cut ~area (P.empty |> P.circle V2.zero 0.1) (I.const col) in Array.map2_exn x y ~f:(fun x y -> I.move (V2.v x y) mark ) |> Array.fold ~init:I.void ~f:I.blend method bbox = Box2.v (V2.v xmin ymin) (V2.v (xmax -. xmin) (ymax -. ymin)) end let rect ?draw ?fill ?(thickness = `normal) ~xmin ~xmax ~ymin ~ymax () = object method render = let sw = V2.v xmin ymin in let nw = V2.v xmin ymax in let ne = V2.v xmax ymax in let se = V2.v xmax ymin in let p = P.empty |> P.sub sw |> P.line nw |> P.line ne |> P.line se |> P.line sw in let outline = match draw with | None -> I.void | Some col -> let area = `O { P.o with P.width = thickness_value thickness ; P.cap = `Square } in I.cut ~area p (I.const col) in let background = match fill with | None -> I.void | Some col -> I.cut ~area:`Anz p (I.const col) in I.blend outline background method bbox = Box2.v (V2.v xmin ymin) (V2.v (xmax -. xmin) (ymax -. ymin)) end let circle ?draw ?fill ?(thickness = `normal) ~x ~y ~radius () = let c = V2.v x y in object method render = let p = P.empty |> P.circle c radius in let outline = match draw with | None -> I.void | Some col -> let area = `O { P.o with P.width = thickness_value thickness ; P.cap = `Square } in I.cut ~area p (I.const col) in let background = match fill with | None -> I.void | Some col -> I.cut ~area:`Anz p (I.const col) in I.blend outline background method bbox = Box2.v_mid c (V2.v (2. *. radius) (2. *. radius)) end let void = object method render = I.void method bbox = Box2.empty end let blend xs = object method render = List.fold xs ~init:I.void ~f:(fun acc p -> I.blend acc p#render) method bbox = List.map xs ~f:(fun x -> x#bbox) |> List.fold ~init:Box2.empty ~f:Box2.union end let blend2 x y = blend [ x ; y ] let bbox x = x#bbox let arrow_head_geometry points = match List.rev points with | [] | [ _ ] -> None | (x1, y1) :: (x2, y2) :: _ -> let tip = V2.v x1 y1 in let top = V2.v x2 y2 in let delta_colinear = V2.(sub top tip |> unit) in let delta_ortho = V2.(delta_colinear |> ortho |> smul 0.3) in let bottom = V2.(add tip delta_colinear) in let wing_up = V2.add bottom delta_ortho in let wing_down = V2.sub bottom delta_ortho in Some ( object method bottom = bottom method tip = tip method wing_up = wing_up method wing_down = wing_down end ) let path ?(col = Color.black) ?(thickness = `normal) ?(arrow_head = false) ?(cap = `Butt) points = let arrow_head = if arrow_head then arrow_head_geometry points else None in object method render = let body = match List.rev points with | [] | [ _ ] -> I.void | (ox, oy) :: (_ :: _ as t) -> let tip = match arrow_head with | None -> V2.v ox oy | Some h -> h#bottom in let path = List.fold t ~init:(P.empty |> P.sub tip) ~f:(fun acc (x, y) -> P.line (V2.v x y) acc ) in let area = `O { P.o with P.width = thickness_value thickness ; cap } in I.cut ~area path (I.const col) and head = match arrow_head with | None -> I.void | Some head -> let path = P.empty |> P.sub head#tip |> P.line head#wing_up |> P.line head#wing_down in I.cut ~area:`Anz path (I.const col) in I.blend head body method bbox = let init = Box2.empty in let init = List.fold points ~init ~f:(fun acc (x, y) -> Box2.add_pt acc (V2.v x y) ) in match arrow_head with | None -> init | Some head -> List.fold [ head#tip ; head#wing_up ; head#wing_down ] ~init ~f:Box2.add_pt end let text ?(col = Color.black) ?(size = 12.) ?(font = Font.default) ?(halign = `middle) ?(valign = `base) ~x ~y text = let font = Lazy.force font in let layout = Vg_text.Layout.make font ~size text in let img = Vg_text.cut ~col:col layout in let width, maxy, miny = Vg_text.Layout.(width layout, maxy layout, miny layout) in let dx = match halign with | `middle -> width /. 2. | `left -> 0. | `right -> width in let dy = match valign with | `base -> 0. | `top -> maxy | `bottom -> miny in object method render = I.move (V2.v (x -. dx) (y -. dy)) img method bbox = let bb = Box2.of_pts V2.(v 0. miny) V2.(v width maxy) in Box2.move (V2.v (x -. dx) (y -. dy)) bb end let translate ?(dx = 0.) ?(dy = 0.) t = object method bbox = Box2.move (V2.v dx dy) (t#bbox) method render = t#render |> I.move (V2.v dx dy) end let scale ?(center = `bbox_center) ?(sx = 1.) ?(sy = 1.) t = object method bbox = let bb = t#bbox in match center with | `bbox_center -> Box2.(v_mid (mid bb) (V2.v (w bb *. sx) (h bb *. sy))) | `origin -> Box2.of_pts (V2.v (Box2.minx bb *. sx) (Box2.maxy bb *. sy)) (V2.v (Box2.maxx bb *. sx) (Box2.miny bb *. sy)) method render = let center = match center with | `bbox_center -> Box2.mid t#bbox | `origin -> V2.zero in t#render |> I.move V2.(neg center) |> I.scale (V2.v sx sy) |> I.move center end let reshape t ~bbox = object method bbox = bbox method render = let src_bbox = t#bbox in let src_center = Box2.mid t#bbox in let dst_center = Box2.mid bbox in let sx = Box2.(w bbox /. w src_bbox) in let sy = Box2.(h bbox /. h src_bbox) in t#render |> I.move V2.(neg src_center) |> I.scale (V2.v sx sy) |> I.move dst_center end let path_of_box2 b = P.empty |> P.line (Box2.bl_pt b) |> P.line (Box2.br_pt b) |> P.line (Box2.tr_pt b) |> P.line (Box2.tl_pt b) |> P.line (Box2.bl_pt b) let crop t b = object method bbox = b method render = I.cut (path_of_box2 b) t#render end let frame t = object method bbox = t#bbox method render = let bb = t#bbox in let sw = Box2.bl_pt bb in let nw = Box2.tl_pt bb in let ne = Box2.tr_pt bb in let se = Box2.br_pt bb in let p = P.empty |> P.sub sw |> P.line nw |> P.line ne |> P.line se |> P.line sw in let area = `O { P.o with P.width = 0.01 ; P.cap = `Square } in I.blend t#render (I.cut ~area p (I.const Color.black)) end (* Tetris-like layout *) module Pileup_layout = struct type block = { bbox : Box2.t ; contents : t ; } let block_intersects b1 b2 = let open Float in let b1 = b1.bbox in let b2 = b2.bbox in Box2.( minx b1 <= minx b2 && minx b2 <= maxx b1 || minx b2 <= minx b1 && minx b1 <= maxx b2 ) let block_compare b1 b2 = let b1 = b1.bbox in let b2 = b2.bbox in Caml.compare Box2.(minx b1, maxx b1) Box2.(minx b2, maxx b2) let make_block contents = { bbox = contents#bbox ; contents ; } let x_overlap_partition = function | [] -> [], [] | h :: t -> let rec loop inside outside last = function | [] -> List.rev (last :: inside), List.rev outside | h :: t -> if block_intersects last h then loop inside (h :: outside) last t else loop (last :: inside) outside h t in loop [] [] h t let make items = let rec loop acc base_y = function | [] -> List.rev acc | items -> let layer, rest = x_overlap_partition items in let layer_height = List.map layer ~f:(fun bl -> Box2.h bl.bbox) |> List.reduce_exn ~f:Float.max in let translated_layer = List.map layer ~f:(fun bl -> translate ~dy:(base_y -. Box2.miny bl.bbox) bl.contents ) in loop (translated_layer :: acc) (base_y +. layer_height) rest in let sorted_blocks = List.map items ~f:make_block |> List.sort ~compare:(fun x y -> block_compare x y) in let layers = match sorted_blocks with | [] -> [] | h :: _ -> loop [] (Box2.maxy h.bbox) sorted_blocks in List.concat layers end let pileup xs = blend (Pileup_layout.make xs) module VStack_layout = struct let make alignment items = let bboxes = List.map items ~f:(fun i -> i#bbox) in let height = List.fold bboxes ~init:0. ~f:(fun acc bb -> acc +. Box2.h bb ) in let justify y pic bbox = let dy = y -. Box2.maxy bbox in let dx = match alignment with | `none -> 0. | `centered -> -. Box2.midx bbox | `left -> -. Box2.minx bbox | `right -> -. Box2.maxx bbox in translate ~dx ~dy pic in List.fold2_exn items bboxes ~init:(height, []) ~f:(fun ((y, acc) as p) pic bbox -> if Box2.is_empty bbox then p else let pic' = justify y pic bbox in (y -. Box2.h bbox, pic' :: acc) ) |> snd |> List.rev end let vstack ?(align = `none) xs = VStack_layout.make align xs |> blend module HStack_layout = struct let make alignment items = let bboxes = List.map items ~f:(fun i -> i#bbox) in let justify x pic bbox = let dx = x -. Box2.minx bbox in let dy = match alignment with | `none -> 0. | `centered -> -. Box2.midy bbox | `top -> -. Box2.maxy bbox | `bottom -> -. Box2.miny bbox in translate ~dx ~dy pic in List.fold2_exn items bboxes ~init:(0., []) ~f:(fun ((x, acc) as p) pic bbox -> if Box2.is_empty bbox then p else let pic' = justify x pic bbox in (x +. Box2.w bbox, pic' :: acc) ) |> snd |> List.rev end let hstack ?(align = `none) xs = HStack_layout.make align xs |> blend end module Plot = struct type t = | Points of { title : string option ; col : Color.t ; shape : point_shape ; x : float array ; y : float array ; } let points ?title ?(col = Color.black) ?(shape = `bullet) x y = Points { title ; col ; shape ; x ; y } let min_x = function | Points { x ; _ } -> Float_array.min x let max_x = function | Points { x ; _ } -> Float_array.max x let min_y = function | Points { y ; _ } -> Float_array.min y let max_y = function | Points { y ; _ } -> Float_array.max y let bb plot = let minx = min_x plot in let miny = min_y plot in Box2.v (V2.v minx miny) (V2.v (max_x plot -. minx) (max_y plot -. miny)) let render ?(width = 10.) ?(height = 6.) plots = match plots with | [] -> Picture.void | _ -> let bb = List.map plots ~f:bb |> List.reduce_exn ~f:Box2.union in let vp = Viewport.linear ~xlim:Box2.(minx bb, maxx bb) ~ylim:Box2.(miny bb, maxy bb) ~size:(width, height) in List.map plots ~f:(function | Points { x ; y ; col ; shape ; _ } -> let x = Array.map x ~f:(Viewport.scale_x vp) in let y = Array.map y ~f:(Viewport.scale_y vp) in Picture.points ~col ~x ~y ~shape () ) |> Picture.blend end type target = [ | `File of string | `Channel of Stdlib.out_channel | `Buffer of Buffer.t ] module Layout = struct type t = | Simple of Picture.t let simple x = Simple x let rec size ?width ?height view = let res w h = w *. 10., h *.10. in match width, height with | Some w, Some h -> res w h | Some w, None -> let h = Box2.h view *. w /. Box2.w view in res w h | None, Some h -> let w = Box2.w view *. h /. Box2.h view in res w h | None, None -> size ~width:10. view let box2_padding alpha b = let w = Box2.w b in let h = Box2.h b in let delta = Float.(min w h * alpha) in Box2.v_mid (Box2.mid b) (V2.v (w +. delta) (h +. delta)) let render ?width ?height format (Simple pic) target = let view = box2_padding 0.01 pic#bbox in let size = size ?width ?height view in let image = pic#render in let renderer = match format with | `pdf -> let otf_font x = Lazy.force x |> Vg_text.Font.data |> Vgr_pdf.otf_font |> function | Ok x -> x | Error _ -> assert false in let font (f : Vg.Font.t) = match f.name with | "DejaVuSansMono" -> otf_font Font.dejavu_sans_mono | "DejaVuSansMono-Bold" -> otf_font Font.dejavu_sans_mono_bold | "DejaVuSansMono-Oblique" -> otf_font Font.dejavu_sans_mono_oblique | "DejaVuSansMono-BoldOblique" -> otf_font Font.dejavu_sans_mono_bold_oblique | "LiberationSans" -> otf_font Font.liberation_sans | "LiberationSans-Bold" -> otf_font Font.liberation_sans_bold | "LiberationSans-Italic" -> otf_font Font.liberation_sans_italic | "LiberationSans-BoldItalic" -> otf_font Font.liberation_sans_bold_italic | _ -> `Sans in Vgr_pdf.target ~font () | `svg -> Vgr_svg.target () in let render target = let r = Vgr.create renderer target in ignore (Vgr.render r (`Image (V2.of_tuple size, view, image))) ; ignore (Vgr.render r `End) in match target with | `File fn -> Out_channel.with_file fn ~f:(fun oc -> render (`Channel oc)) | (`Channel _ | `Buffer _) as target -> render target end
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