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/iset.ml.html
Source file iset.ml
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(* Copyright 2003 Yamagata Yoriyuki. distributed with LGPL *) (* Modified by Edgar Friendly <thelema314@gmail.com> *) (* Modified by Philippe Veber <philippe.veber@gmail.com> *) (* Copyright 2003 Yamagata Yoriyuki. distributed with LGPL *) (* Modified by Edgar Friendly <thelema314@gmail.com> *) module Int = Int open CFStream module BatAvlTree = struct type 'a tree = | Empty | Node of 'a tree * 'a * 'a tree * int (* height *) let empty = Empty let is_empty = function | Empty -> true | Node _ -> false let singleton_tree x = Node (Empty, x, Empty, 1) let left_branch = function | Empty -> raise Caml.Not_found | Node (l, _, _, _) -> l let right_branch = function | Empty -> raise Caml.Not_found | Node (_, _, r, _) -> r let root = function | Empty -> raise Caml.Not_found | Node (_, v, _, _) -> v let height = function | Empty -> 0 | Node (_, _, _, h) -> h let create l v r = let h' = 1 + Int.max (height l) (height r) in assert (abs (height l - height r ) < 2); Node (l, v, r, h') (* Assume |hl - hr| < 3 *) let bal l v r = let hl = height l in let hr = height r in if hl >= hr + 2 then match l with | Empty -> assert false | Node (ll, lv, lr, _) -> if height ll >= height lr then create ll lv (create lr v r) else match lr with | Empty -> assert false | Node (lrl, lrv, lrr, _) -> create (create ll lv lrl) lrv (create lrr v r) else if hr >= hl + 2 then match r with | Empty -> assert false | Node (rl, rv, rr, _) -> if height rr >= height rl then create (create l v rl) rv rr else match rl with | Empty -> assert false | Node (rll, rlv, rlr, _) -> create (create l v rll) rlv (create rlr rv rr) else create l v r let rec add_left v = function | Empty -> Node (Empty, v, Empty, 1) | Node (l, v', r, _) -> bal (add_left v l) v' r let rec add_right v = function | Empty -> Node (Empty, v, Empty, 1) | Node (l, v', r, _) -> bal l v' (add_right v r) (* No assumption of height of l and r. *) let rec make_tree l v r = match l , r with | Empty, _ -> add_left v r | _, Empty -> add_right v l | Node (ll, lv, lr, lh), Node (rl, rv, rr, rh) -> if lh > rh + 1 then bal ll lv (make_tree lr v r) else if rh > lh + 1 then bal (make_tree l v rl) rv rr else create l v r (* Utilities *) let rec split_leftmost = function | Empty -> raise Caml.Not_found | Node (Empty, v, r, _) -> (v, r) | Node (l, v, r, _) -> let v0, l' = split_leftmost l in (v0, make_tree l' v r) let rec split_rightmost = function | Empty -> raise Caml.Not_found | Node (l, v, Empty, _) -> (v, l) | Node (l, v, r, _) -> let v0, r' = split_rightmost r in (v0, make_tree l v r') let rec concat t1 t2 = match t1, t2 with | Empty, _ -> t2 | _, Empty -> t1 | Node (l1, v1, r1, h1), Node (l2, v2, r2, h2) -> if h1 < h2 then make_tree (concat t1 l2) v2 r2 else make_tree l1 v1 (concat r1 t2) let rec iter proc = function | Empty -> () | Node (l, v, r, _) -> iter proc l; proc v; iter proc r let rec fold f t init = match t with | Empty -> init | Node (l, v, r, _) -> let x = fold f l init in let x = f v x in fold f r x (* FIXME: this is nlog n because of the left nesting of appends *) let rec to_stream = function | Empty -> Stream.empty () | Node (l, v, r, _) -> Stream.append (Stream.append (Stream.of_lazy (lazy (to_stream l))) (Stream.singleton v)) (Stream.of_lazy (lazy (to_stream r))) end include BatAvlTree type t = (int * int) tree let rec mem s (n:int) = if is_empty s then false else let v1, v2 = root s in if n < v1 then mem (left_branch s) n else if v1 <= n && n <= v2 then true else mem (right_branch s) n let rec intersects_range s i j = if i > j then raise (Invalid_argument "iset_intersects_range") ; if is_empty s then false else let v1, v2 = root s in if j < v1 then intersects_range (left_branch s) i j else if v2 < i then intersects_range (right_branch s) i j else true let rec add s n = if is_empty s then make_tree empty (n, n) empty else let (v1, v2) as v = root s in let s0 = left_branch s in let s1 = right_branch s in if v1 <> Int.min_value && n < v1 - 1 then make_tree (add s0 n) v s1 else if v2 <> Int.max_value && n > v2 + 1 then make_tree s0 v (add s1 n) else if n + 1 = v1 then if not (is_empty s0) then let (u1, u2), s0' = split_rightmost s0 in if u2 <> Int.max_value && u2 + 1 = n then make_tree s0' (u1, v2) s1 else make_tree s0 (n, v2) s1 else make_tree s0 (n, v2) s1 else if v2 + 1 = n then if not (is_empty s1) then let (u1, u2), s1' = split_leftmost s1 in if n <> Int.max_value && n + 1 = u1 then make_tree s0 (v1, u2) s1' else make_tree s0 (v1, n) s1 else make_tree s0 (v1, n) s1 else s let rec from s ~n = if is_empty s then empty else let (v1, v2) as v = root s in let s0 = left_branch s in let s1 = right_branch s in if n < v1 then make_tree (from s0 ~n) v s1 else if n > v2 then from s1 ~n else make_tree empty (n, v2) s1 let after s ~n = if n = Int.max_value then empty else from s ~n:(n + 1) let rec until s ~n = if is_empty s then empty else let (v1, v2) as v = root s in let s0 = left_branch s in let s1 = right_branch s in if n > v2 then make_tree s0 v (until s1 ~n) else if n < v1 then until s0 ~n else make_tree s0 (v1, n) empty let before s ~n = if n = Int.min_value then empty else until s ~n:(n - 1) let add_range s n1 n2 = if n1 > n2 then invalid_arg (Printf.sprintf "ISet.add_range - %d > %d" n1 n2) else let n1, l = if n1 = Int.min_value then n1, empty else let l = until s ~n:(n1 - 1) in if is_empty l then n1, empty else let (v1, v2), l' = split_rightmost l in if v2 + 1 = n1 then v1, l' else n1, l in let n2, r = if n2 = Int.max_value then n2, empty else let r = from s ~n:(n2 + 1) in if is_empty r then n2, empty else let (v1, v2), r' = split_leftmost r in if n2 + 1 = v1 then v2, r' else n2, r in make_tree l (n1, n2) r let singleton n = singleton_tree (n, n) let rec remove s n = if is_empty s then empty else let (v1, v2) as v = root s in let s1 = left_branch s in let s2 = right_branch s in if n < v1 then make_tree (remove s1 n) v s2 else if n = v1 then if v1 = v2 then concat s1 s2 else make_tree s1 (v1 + 1, v2) s2 else if n > v1 && n < v2 then let s = make_tree s1 (v1, n - 1) empty in make_tree s (n + 1, v2) s2 else if n = v2 then make_tree s1 (v1, v2 - 1) s2 else make_tree s1 v (remove s2 n) let remove_range s n1 n2 = if n1 > n2 then invalid_arg "ISet.remove_range" else concat (before s ~n:n1) (after s ~n:n2) let rec union s1 s2 = if is_empty s1 then s2 else if is_empty s2 then s1 else let s1, s2 = if height s1 > height s2 then s1, s2 else s2, s1 in let n1, n2 = root s1 in let l1 = left_branch s1 in let r1 = right_branch s1 in let l2 = before s2 ~n:n1 in let r2 = after s2 ~n:n2 in let n1, l = if n1 = Int.min_value then n1, empty else let l = union l1 l2 in if is_empty l then n1, l else let (v1, v2), l' = split_rightmost l in (* merge left *) if v2 + 1 = n1 then v1, l' else n1, l in let n2, r = if n1 = Int.max_value then n2, empty else let r = union r1 r2 in if is_empty r then n2, r else let (v1, v2), r' = split_leftmost r in (* merge right *) if n2 + 1 = v1 then v2, r' else n2, r in make_tree l (n1, n2) r (*$= union & ~cmp:equal ~printer:(IO.to_string print) (union (of_list [3,5]) (of_list [1,3])) (of_list [1,5]) (union (of_list [3,5]) (of_list [1,2])) (of_list [1,5]) (union (of_list [3,5]) (of_list [1,5])) (of_list [1,5]) (union (of_list [1,5]) (of_list [3,5])) (of_list [1,5]) (union (of_list [1,2]) (of_list [4,5])) (of_list [1,2;4,5]) *) let rec inter s1 s2 = if is_empty s1 then empty else if is_empty s2 then empty else let s1, s2 = if height s1 > height s2 then s1, s2 else s2, s1 in let n1, n2 = root s1 in let l1 = left_branch s1 in let r1 = right_branch s1 in let l2 = before s2 ~n:n1 in let r2 = after s2 ~n:n2 in let m = until (from s2 ~n:n1) ~n:n2 in concat (concat (inter l1 l2) m) (inter r1 r2) (*$= inter & ~cmp:equal ~printer:(IO.to_string print) (inter (of_list [1,5]) (of_list [2,3])) (of_list [2,3]) (inter (of_list [1,4]) (of_list [2,6])) (of_list [2,4]) *) let rec compl_aux n1 n2 s = if is_empty s then add_range empty n1 n2 else let v1, v2 = root s in let l = left_branch s in let r = right_branch s in let l = if v1 = Int.min_value then empty else compl_aux n1 (v1 - 1) l in let r = if v2 = Int.max_value then empty else compl_aux (v2 + 1) n2 r in concat l r let compl s = compl_aux Int.min_value Int.max_value s let diff s1 s2 = inter s1 (compl s2) let rec compare_aux x1 x2 = match x1, x2 with [], [] -> 0 | `Set s :: rest, x -> if is_empty s then compare_aux rest x2 else let l = left_branch s in let v = root s in let r = right_branch s in compare_aux (`Set l :: `Range v :: `Set r :: rest) x | _x, `Set s :: rest -> if is_empty s then compare_aux x1 rest else let l = left_branch s in let v = root s in let r = right_branch s in compare_aux x1 (`Set l :: `Range v :: `Set r :: rest) | `Range ((v1, v2)) :: rest1, `Range ((v3, v4)) :: rest2 -> let sgn = Int.compare v1 v3 in if sgn <> 0 then sgn else let sgn = Int.compare v2 v4 in if sgn <> 0 then sgn else compare_aux rest1 rest2 | [], _ -> ~-1 | _, [] -> 1 let compare s1 s2 = compare_aux [`Set s1] [`Set s2] let equal s1 s2 = compare s1 s2 = 0 let rec subset s1 s2 = if is_empty s1 then true else if is_empty s2 then false else let v1, v2 = root s2 in let l2 = left_branch s2 in let r2 = right_branch s2 in let l1 = before s1 ~n:v1 in let r1 = after s1 ~n:v2 in (subset l1 l2) && (subset r1 r2) let fold_range s ~init ~f = BatAvlTree.fold (fun (n1, n2) x -> f n1 n2 x) s init let fold s ~init ~f = let rec g n1 n2 a = if n1 = n2 then f n1 a else g (n1 + 1) n2 (f n1 a) in fold_range ~f:g s ~init let iter s ~f = fold s ~init:() ~f:(fun n () -> f n) let iter_range s ~f = BatAvlTree.iter (fun (n1, n2) -> f n1 n2) s let for_all s ~f = let rec test_range n1 n2 = if n1 = n2 then f n1 else f n1 && test_range (n1 + 1) n2 in let rec test_set s = if is_empty s then true else let n1, n2 = root s in test_range n1 n2 && test_set (left_branch s) && test_set (right_branch s) in test_set s (*$T for_all for_all (fun x -> x < 10) (of_list [1,3;2,7]) not (for_all (fun x -> x = 5) (of_list [4,5])) *) let exists s ~f = let rec test_range n1 n2 = if n1 = n2 then f n1 else f n1 || test_range (n1 + 1) n2 in let rec test_set s = if is_empty s then false else let n1, n2 = root s in test_range n1 n2 || test_set (left_branch s) || test_set (right_branch s) in test_set s (*$T exists exists (fun x -> x = 5) (of_list [1,10]) not (exists (fun x -> x = 5) (of_list [1,3;7,10])) *) let filter_range p n1 n2 a = let rec loop n1 n2 a = function None -> if n1 = n2 then make_tree a (n1, n1) empty else loop (n1 + 1) n2 a (if p n1 then Some n1 else None) | Some v1 as x -> if n1 = n2 then make_tree a (v1, n1) empty else if p n1 then loop (n1 + 1) n2 a x else loop (n1 + 1) n2 (make_tree a (v1, n1 - 1) empty) None in loop n1 n2 a None let filter s ~f = fold_range s ~f:(filter_range f) ~init:empty let partition_range p n1 n2 (a, b) = let rec loop n1 n2 acc = let acc = let a, b, (v, n) = acc in if Bool.(p n1 = v) then acc else if v then (make_tree a (n, n1) empty, b, (not v, n1)) else (a, make_tree b (n, n1) empty, (not v, n1)) in if n1 = n2 then let a, b, (v, n) = acc in if v then (make_tree a (n, n1) empty, b) else (a, make_tree b (n, n1) empty) else loop (n1 + 1) n2 acc in loop n1 n2 (a, b, (p n1, n1)) let partition s ~f = fold_range ~f:(partition_range f) s ~init:(empty, empty) let cardinal s = fold_range ~f:(fun n1 n2 c -> c + n2 - n1 + 1) s ~init:0 (*$T cardinal cardinal (of_list [1,3;5,9]) = 8 *) let rev_ranges s = fold_range ~f:(fun n1 n2 a -> (n1, n2) :: a) s ~init:[] let rec burst_range n1 n2 a = if n1 = n2 then n1 :: a else burst_range n1 (n2 - 1) (n2 :: a) let elements s = let f a (n1, n2) = burst_range n1 n2 a in List.fold_left ~f ~init:[] (rev_ranges s) (*$Q ranges;of_list (Q.list (Q.pair Q.int Q.int)) (fun l -> \ let norml = List.map (fun (x,y) -> if x < y then (x,y) else (y,x)) l in \ let set = of_list norml in \ equal set (ranges set |> of_list) \ ) *) let ranges s = List.rev (rev_ranges s) let min_elt s = let (n, _), _ = split_leftmost s in n let max_elt s = let (_, n), _ = split_rightmost s in n let choose s = fst (root s) let of_list l = List.fold_left ~f:(fun s (lo,hi) -> add_range s lo hi) ~init:empty l let of_stream e = Stream.fold ~f:(fun s (lo,hi) -> add_range s lo hi) ~init:empty e
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