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/Accu/index.html

Module `Biocaml_unix.Accu`

A datastructure (based on Hashtbl) to accumulate values.

An Accu.t can be seen as a generalized histogram: samples are mapped to bins, and each bin has a corresponding value which may be its size or its contents depending on the need.

Generic API

type ('sample, 'bin, 'increment, 'accu) t

General type for accumulators: 'samples are mapped to 'bins, and the 'accumulated value for a 'bin is updated with an 'increment

val create : 
  ?n:int ->
  bin:('a -> 'b) ->
  zero:'d ->
  add:('c -> 'd -> 'd) ->
  unit ->
  ('a, 'b, 'c, 'd) t

create ~n ~zero ~bin ~add creates an accumulator, which maps instances to bins with bin, uses zero as a neutral element (that is the value associated to a bin before any value has been added to it) and updates the value of a bin with add. n is an estimation of the maximum number of bins.

val add : ('a, 'b, 'c, 'd) t -> 'a -> 'c -> unit

add accu x y updates the value in accu for the bin of x by an increment y

val stream : ('a, 'b, 'c, 'd) t -> ('b * 'd) Stream.t

val to_alist : ('a, 'b, 'c, 'd) t -> ('b * 'd) list

val get : ('a, 'b, 'c, 'd) t -> 'b -> 'd option

get accu x returns the value associated to b in accu.

Counters and histograms

module Counter : sig ... end

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

val product : 
  ?filter:('a -> 'b -> bool) ->
  ('a -> 'b -> 'c) ->
  'a list ->
  'b list ->
  ('c * int) Stream.t

product filter f l1 l2 computes an histogram of values returned by f when it is applied for all combinations of elements in l1 and l2 such that the predicate filter is true

Relation

module Relation : sig ... end

val relation : ('a * 'b) Stream.t -> ('a * 'b list) Stream.t

module Bins : sig ... end

On This Page

Generic API
Counters and histograms
Relation