package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.10.0.tar.gz

md5=497e3f2f7128a6ca347d66848da38a3d

sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

doc/biocaml.unix/Biocaml_unix/Interval_tree/index.html

Module `Biocaml_unix.Interval_tree`

Interval tree (data structure)

An interval tree is a collection of integer-bounded intervals labeled by a value.

For a brief description of the implementation, see the matching Wikipedia article

type 'a t

exception Empty_tree

Accessors

val is_empty : 'a t -> bool

val cardinal : 'a t -> int

val intersects : 'a t -> low:int -> high:int -> bool

intersects a b t returns true if one interval in t intersects with the interval [a;b].

Constructors

val empty : 'a t

the empty tree

val add : 'a t -> low:int -> high:int -> data:'a -> 'a t

add lo hi v t adds the interval (lo, hi) labeled with value v to the contents of t. Note that in contrast to sets, identical intervals (even with identical labels) may be *repeated* in an interval tree. E.g., add 1 2 () (add 1 2 ()) contains 2 intervals.

Conversion

val elements : 'a t -> (int * int * 'a) list

val to_stream : 'a t -> (int * int * 'a) Stream.t

val to_backwards_stream : 'a t -> (int * int * 'a) Stream.t

Searching and filtering

val find_closest : int -> int -> 'a t -> int * int * 'a * int

find_closest lo hi t returns the interval in t which is at minimal distance of the interval [lo;hi]. The resulting tuple contains from left to right, left-end of the interval, right-end of the interval, value associated to the interval and distance to the interval given in argument. Overlapping intervals are at distance 0 of each other.

Raises Empty_tree if t is empty

val find_intersecting_elem : int -> int -> 'a t -> (int * int * 'a) Stream.t

find_intersecting_elem a b t is equivalent to Stream.filter ~f:(fun (x,y,_) -> intersects x y t) (stream t) but is more efficient.

val filter_overlapping : 'a t -> low:int -> high:int -> 'a t

Create an interval tree with the elements which overlap with [low, high].

Misc

val print : 'a t -> unit

Used for debugging purpose, should be removed in the long run

val check_integrity : 'a t -> unit