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Module Biocaml_genomeMap (.ml)

Indicator function on a genome

module Biocaml_genomeMap:
sig
type range = Biocaml_range.t 
type 'a location = 'a * range

Indicator function on a genome

module Selection:
sig
type 'a t 
val inter : 'a t ->
       'a t -> 'a t
val union : 'a t ->
       'a t -> 'a t
val diff : 'a t ->
       'a t -> 'a t
val size : 'a t -> int
val intersects : 'a Biocaml_genomeMap.location -> 'a t -> bool
intersects loc sel returns true if loc has a non-empty intersection with sel, and false otherwise.
val intersection_size : 'a Biocaml_genomeMap.location -> 'a t -> int
val to_stream : 'a t -> 'a Biocaml_genomeMap.location Stream.t
val of_stream : 'a Biocaml_genomeMap.location Stream.t -> 'a t
of_stream e computes a selection as the union of the locations contained in e
end
module type Signal =
sig
type ('a, 'b) t 
val make : ('b list -> 'c) ->
       ('a Biocaml_genomeMap.location * 'c) Stream.t ->
       ('a, 'c) t
val eval : 'a -> int -> ('a, 'b) t -> 'b
function evaluation at some point in the genome
val fold : ('a -> Biocaml_genomeMap.range -> 'b -> 'c -> 'c) ->
       ('a, 'b) t -> 'c -> 'c
folds on constant intervals of the function, in increasing order
val to_stream : ('a, 'b) t ->
       ('a Biocaml_genomeMap.location * 'b) Stream.t
enumeration over all constant intervals of the function, in increasing order
end
Partial function over the genome: each base may be associated to a value.

A set of locations

module LSet:
sig
type 'a t 
val to_stream : 'a t -> 'a Biocaml_genomeMap.location Stream.t
val of_stream : 'a Biocaml_genomeMap.location Stream.t -> 'a t
val intersects : 'a Biocaml_genomeMap.location -> 'a t -> bool
intersects loc lmap returns true if loc has a non-empty intersection with one of the locations in lmap, and returns false otherwise
val closest : 'a Biocaml_genomeMap.location ->
       'a t -> ('a Biocaml_genomeMap.location * int) option
closest loc lset returns the location in lset that is the closest to loc, along with the actual (minimal) distance. Returns None if there is no location in lset that comes from the same sequence than loc.
val intersecting_elems : 'a Biocaml_genomeMap.location ->
       'a t -> 'a Biocaml_genomeMap.location Stream.t
intersecting_elems loc lset returns an enumeration of all locations in lset that intersect loc.
end

A set of locations with an attached value on each of them

module LMap:
sig
type ('a, 'b) t 
val to_stream : ('a, 'b) t ->
       ('a Biocaml_genomeMap.location * 'b) Stream.t
val of_stream : ('a Biocaml_genomeMap.location * 'b) Stream.t ->
       ('a, 'b) t
val intersects : 'a Biocaml_genomeMap.location -> ('a, 'b) t -> bool
intersects loc lmap returns true if loc has a non-empty intersection with one of the locations in lmap, and returns false otherwise
val closest : 'a Biocaml_genomeMap.location ->
       ('a, 'b) t ->
       ('a Biocaml_genomeMap.location * 'b * int) option
closest loc lmap returns the location in lmap that is the closest to loc, along with its annotation and the actual (minimal) distance. Returns None if there is no location in lmap that comes from the same sequence than loc.
val intersecting_elems : 'a Biocaml_genomeMap.location ->
       ('a, 'b) t ->
       ('a Biocaml_genomeMap.location * 'b) Stream.t
intersecting_elems loc lmap returns an enumeration of elements in lmap whose location intersects with loc.
end
module type LMap_spec =
sig
type ('a, 'b) t 
val make : ('a Biocaml_genomeMap.location * 'b) Stream.t ->
       ('a, 'b) t
val fold : ('a -> Biocaml_genomeMap.range -> 'b -> 'c -> 'c) ->
       ('a, 'b) t -> 'c -> 'c
fold guaranteed on increasing order keywise, and for each key
val pwfold : ('a -> Biocaml_genomeMap.range -> 'b list -> 'c -> 'c) ->
       ('a, 'b) t -> 'c -> 'c
a constant interval of an LMap lm is a range intersecting lm and that do not contain any start or end of a range from lm. A maximal constant interval is a constant interval, maximum for inclusion. pwfold f lm init folds on maximal constant intervals of lm, in increasing order
val intersects : 'a Biocaml_genomeMap.location ->
       ('a, 'b) t -> bool
val to_stream : ('a, 'b) t ->
       ('a Biocaml_genomeMap.location * 'b) Stream.t
val union : ('a, 'b) t ->
       ('a, 'b) t ->
       ('a, 'b) t
val add : 'a Biocaml_genomeMap.location ->
       'b ->
       ('a, 'b) t ->
       ('a, 'b) t
end
A set of locations with an attached value on each of them
end