package biotk

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biotk
- Biotk
  - Alphabet
    
    Make
    
    _
    
    S
  - Amino_acid
  - Bai
  - Bam
    
    Alignment0
    
    Header
  - Bam_iterator
  - Bamstats
    
    Chr_histogram
    
    Fragment_length_histogram
  - Bed
    
    Bed3
    
    Item
    
    Bed4
    
    Item
    
    Bed5
    
    Item
    
    Bed6
    
    Item
    
    Item
    
    S
  - Bgzf
  - Cisbp
    
    Motif
    
    TF_information
  - Dataframe
    
    Ez
    
    Parser
  - Dna_sequence
    
    Parser
    
    Parser_of_char
    
    _
  - Encode
    
    Experiment_list
  - Fasta
  - Fastq
    
    Stats
  - FeatureCounts
    
    Summary
    
    Tsv
    
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    Direct
  - GAnnot
    
    LAssoc
    
    LMap
    
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    Selection
  - GLoc
    
    Map
    
    Diff
    
    Key
    
    Provide_bin_io
    
    Key
    
    Provide_hash
    
    Provide_of_sexp
    
    Key
    
    Set
    
    Diff
    
    Elt
    
    Provide_bin_io
    
    Elt
    
    Provide_hash
    
    Provide_of_sexp
    
    Elt
  - Gcf
  - Gene
    
    Transcript
  - Gff
    
    Annotation
    
    GFF2
    
    Item
    
    GFF3
    
    Item
    
    Record
    
    S
    
    Item
  - ISet
  - Ibed
  - Idr
    
    Broad_output
    
    Row
    
    Narrow_output
    
    Row
  - Igv
    
    Statement
    
    proxy
  - Interval_tree
  - Interval_union
  - Jaspar
  - Let_syntax
    
    Result
  - Line
  - Line_oriented
    
    Item
    
    Make
    
    Item
    
    Parser
    
    S
  - List1
  - Macs
    
    Xls
  - Macs2
    
    Broad_peaks
    
    Xls
  - Meme
    
    Motif_format
  - Misc
  - NarrowPeak
    
    Item
  - Ncbi_genome
    
    Assembly_summary
  - Nucleotide
  - Phred_score
  - Phylo_tree_draw
  - Profile_matrix
    
    DNA
    
    Make
    
    _
    
    Protein
    
    S
  - Pwm
  - Pwm_stats
    
    TFM_pvalue
  - RanT
  - Range
  - Sam
    
    Flags
  - Solexa_score
  - Ucsc_genome_browser
    
    Chrom_size
    
    Fields
    
    Direct
  - Utils
  - Wfa
    
    Make
    
    Profile
    
    Score
    
    Symbol
    
    Nucleotide
    
    Nucleotide_IUPAC
    
    Nucleotide_frequency
    
    PSSM
    
    Profile
    
    S
    
    Score
    
    Symbol
biotk.croquis
- Biotk_croquis
  - Croquis
    
    Axis
    
    Colormap
    
    Font
    
    Plot
    
    Viewport
  - Font_data
    
    Internal
  - Vg_text
    
    Font
    
    Layout
biotk.pipes
- Biotk_pipes
  - Pipe
    
    Make
    
    M
    
    Monad_infix
    
    Monad
    
    S
    
    Monad_infix
biotk.pipes.unix
- Biotk_pipes_unix
  - Pipe
    
    Monad_infix

Legend:
Library
Module
Module type
Parameter
Class
Class type

DIET : Discrete Interval Encoding Trees

Sets of integers represented as ranges

This data structure is efficient for large sets of integers where many adjacent integers are all part of the set. This will have higher overhead for sets with lots of point elements, but will be much more efficient for sets containing mostly ranges.

type t

val empty : t

The empty set

val is_empty : t -> bool

Test whether a set is empty, returns true if the set is empty.

val mem : t -> int -> bool

test whether a given int is a member of the set

val add : t -> int -> t

Add the given int to the set, returning a new set

val add_range : t -> int -> int -> t

add_range t lo hi adds the range of integers lo, hi (including both endpoints) to the given set, returning a new set

raises Invalid_argument
if lo > hi

val intersects_range : t -> int -> int -> bool

val singleton : int -> t

Return the singleton set containing only the given element

val remove : t -> int -> t

Remove an element from the given set, returning a new set

val remove_range : t -> int -> int -> t

remove_range lo hi t removes a range of elements from the given set, returning a new set

raises Invalid_argument
if lo > hi

val union : t -> t -> t

Compute the union of two sets. This is the set whose elements are those elements in either input set.

val inter : t -> t -> t

Compute the intersection of two sets. This is the set whose elements are those in *both* of the input sets.

val diff : t -> t -> t

Compute the difference between two sets. This is the set of elements that are in the first but not in the second. Unlike union and inter, order matters here.

val compl : t -> t

Create the complement of the given set - i.e. the set of all values not in the input set.

val compare : t -> t -> int

Compare two sets. It is not safe to use the polymorphic (<) and related functions to compare these sets, as the tree representation used can balance in multiple ways.

val equal : t -> t -> bool

Test whether two sets are equal. It is not safe to use the polymorphic (=) on these sets, as the same set can have multiple representations depending on how it was built.

val subset : t -> t -> bool

subset t u returns true if t is a subset of u

val from : t -> n:int -> t

from ~n t returns the portion of t in the range n, max_int

val after : t -> n:int -> t

after ~n t returns the portion of t in the range n+1, max_int

val until : t -> n:int -> t

until ~n t returns the portion of t in the range min_int, n

val before : t -> n:int -> t

before x t returns the portion of t in the range min_int, n-1

val iter : t -> f:(int -> unit) -> unit

iter f t calls f once for each element of t

val iter_range : t -> f:(int -> int -> unit) -> unit

iter_range ~f t calls f once for each contiguous range of t. The contiguous ranges of a set are sequences of adjacent integers all part of the set.

val fold : t -> init:'a -> f:(int -> 'a -> 'a) -> 'a

fold f t x0 returns the final result of merging each element of t into x0 using merge function f

val fold_range : t -> init:'a -> f:(int -> int -> 'a -> 'a) -> 'a

As fold, but operates on contiguous ranges

val for_all : t -> f:(int -> bool) -> bool

Tests whether a predicate applies to all elements of the set

val exists : t -> f:(int -> bool) -> bool

Test whether some element of a set satisfies a predicate

val filter : t -> f:(int -> bool) -> t

Builds the subset of those elements that satisfy the predicate

val partition : t -> f:(int -> bool) -> t * t

partitions the input set into two sets with elements that satisfy the predicate and those that don't

val cardinal : t -> int

Returns the number of elements in the set

val elements : t -> int list

Returns a list of all elements in the set

val ranges : t -> (int * int) list

Returns a list of all contiguous ranges in the set

val min_elt : t -> int

Returns the minimum element in the set

val max_elt : t -> int

Returns the maximum element in the set

val choose : t -> int

Returns some element in the set

val to_seq : t -> (int * int) Stdlib.Seq.t

Enumerates all contiguous ranges in the set

val of_seq : (int * int) Stdlib.Seq.t -> t

val of_list : (int * int) list -> t

Build a ISet.t out of a list or enum of ranges