package biocaml

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in-package search v0.2.0

The OCaml Bioinformatics Library

Install

Dune Dependency

github.com Readme Edit opam file Versions (5)

Authors

Maintainers

P

philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

doc/biocaml.ez/Biocaml_ez/Range/index.html

Module `Biocaml_ez.Range`Source

include module type of struct include Biocaml_unix.Range end

Sourcetype t = private Biocaml_unix.Range.t = {

lo : int;
hi : int;

}

Type of a range.

include Ppx_compare_lib.Comparable.S with type t := t

Sourceval compare : t Base__Ppx_compare_lib.compare

include Sexplib0.Sexpable.S with type t := t

Sourceval t_of_sexp : Sexplib0.Sexp.t -> t

Sourceval sexp_of_t : t -> Sexplib0.Sexp.t

Sourceval make_unsafe : int -> int -> t

Sourceval size : t -> int

size v returns the number of integers in v, i.e. v.hi - v.lo + 1.

Sourceval member : t -> int -> bool

member t k returns true if t contains k.

Sourceval to_string : t -> string

String representation of an range, intended only for human legibility.

Sourceval to_list : t -> int list

to_list v returns the set of integers contained in v, in ascending order.

Sourceval overlap : t -> t -> int

overlap u v returns amount of overlap between two ranges. A positive value indicates number of integers common to u and v. A negative value indicates the number of integers in between non-overlapping ranges. A zero value means the ranges are exactly adjacent to each other. The relation is symmetric.

Sourceval gap : t -> t -> int

gap u v returns the size of the gap between u and v. It is equivalent to the negative of overlap.

Set Operations

Sourceval union : t -> t -> [ `Joint of t | `Disjoint of t * t ]

union u v returns the range(s) representing the union of u and v. If u and v overlap, their union can be represented as a single range. If not, their union is a disjoint combination of two ranges.

Sourceval intersect : t -> t -> t option

intersect u v returns the range representing the intersection of u and v. Return None if intersection is empty.

Positional Range

Positional means an range is viewed as coming either before or after another.

Sourceval before : t -> t -> bool

before u v is true if strict_before u v || equal u v.

Sourceval after : t -> t -> bool

after u v is equivalent to before v u.

Sourceval strict_before : t -> t -> bool

strict_before u v is true if u.lo < v.lo && u.hi < v.hi.

Sourceval strict_after : t -> t -> bool

strict_after u v is equivalent to strict_before v u.

Sourceval compare_positional : t -> t -> int option

compare_positional u v returns -1 if u is strictly before v, 0 if u is equal to v, +1 if u is strictly after v, and returns None otherwise.

Containment Range

Containment means a range is viewed as being inside, or a subset of, another.

Sourceval subset : t -> t -> bool

subset u v is true if u is a subset of v.

Sourceval superset : t -> t -> bool

superset u v is true if u is a superset of v.

Sourceval strict_subset : t -> t -> bool

strict_subset u v is true if u is a strict subset of v.

Sourceval strict_superset : t -> t -> bool

strict_superset u v is true if u is a strict superset of v.

Sourceval compare_containment : t -> t -> int option

compare_containment u v returns -1 if u is a strict subset of v, 0 if u is equal to v, +1 if u is a strict superset of v, and returns None otherwise.

Range Lists

Sourceval any_overlap : t list -> bool

Return true if any pair of given ranges overlap each other.

Sourceval all_positional : t list -> bool

Return true if all pairs of given ranges are positionally comparable.

Sourceval max_gap_of_positional : t list -> int

Return maximum gap between adjacent pairs of given ranges. Raise Failure if any pairs of given ranges not positionally comparable, or if given less than two ranges.

More Specialized Operations

Source

val find_min_range : 
  ?init_direction:string ->
  t ->
  (t -> bool) ->
  int ->
  t option

find_min_range v pred i finds the minimum sized range within v centered around i that satisfies pred. Successively larger ranges are created starting from [i, i] and the first one to satisfy pred is returned. None is returned if the given range v itself is reached and pred still fails. Raise Failure if i not within v.

The first range tried is [i, i], by default the second is [i, i+1], the third [i-1, i+1], the fourth [i-1, i+2], and so on. The optional init_direction must be either "fwd" or "rev". If "fwd", which is the default, the range size is initially increased in the forward direction. If "rev", the second range tried will be [i-1, i]. If the range boundary is reached on either side, the size continues to be increased by incrementing on the opposing side.

Sourceval expand_assoc_list : (t * 'a) list -> (int * 'a list) list

exp_assoc_list dat returns a list associating each integer i with the list of values associated with all ranges overlapping i in dat. The set of integers considered is the union of all in given dat.

Sourceval find_regions : ?max_gap:int -> ('a -> bool) -> (t * 'a) list -> t list

TO DO: fill in this documentation. For now see Math.find_regions.

Sourceval make_random : t -> t

make_random t returns a random range that is a subset of t. May raise Failure if given range bounds exceed largest value handled by Random module.

Sourceval make : int -> int -> t