package biotk

You can search for identifiers within the package.

in-package search v0.2.0

package biotk

biotk
- Biotk
  - Bai
  - Bam_iterator
  - Bed
    
    Bed3
    
    Record
    
    Bed4
    
    Record
    
    Bed5
    
    Record
    
    Bed6
    
    Record
    
    Record
    
    S
  - Cisbp
    
    Motif
    
    TF_information
  - Dataframe
    
    Ez
  - Dna_sequence
    
    Parser
    
    Parser_of_char
    
    P
  - Encode
    
    Experiment_list
  - Fasta
  - Fastq
    
    Stats
  - FeatureCounts
    
    Summary
    
    Tsv
    
    Fields
    
    Direct
  - GAnnot
    
    LAssoc
    
    LMap
    
    LSet
    
    Selection
  - GLoc
    
    Map
    
    Key
    
    Provide_hash
    
    Provide_of_sexp
    
    Key
    
    Tree
    
    Provide_of_sexp
    
    K
    
    Set
    
    Elt
    
    Named
    
    Provide_hash
    
    Provide_of_sexp
    
    Elt
    
    Tree
    
    Named
    
    Provide_of_sexp
    
    Elt
  - Gcf
  - Gene
    
    Transcript
  - Gff
    
    Item
    
    Record
  - Gtf
    
    Annotation
    
    Item
    
    Record
  - Idr
    
    Broad_output
    
    Row
    
    Narrow_output
    
    Row
  - Igv
    
    Statement
    
    proxy
  - Interval_union
  - Jaspar
  - Let_syntax
    
    Result
  - Line_oriented
    
    Item
    
    Make
    
    Item
    
    S
  - List1
  - Macs
    
    Xls
  - Macs2
    
    Broad_peaks
    
    Xls
  - Misc
  - NarrowPeak
    
    Item
  - Ncbi_genome
    
    Assembly_summary
  - Nucleotide
  - Phylo_tree_draw
  - Pipe_parsers
    
    Monad_infix
  - Profile_matrix
    
    Alphabet
    
    DNA
    
    Make
    
    A
    
    S
  - Pwm
  - Pwm_stats
    
    TFM_pvalue
  - Range
  - Sam
  - 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
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

include Core_kernel.Set_intf.Make_S_plain_tree(Elt).S

type t = (t, Elt.comparator_witness) Core_kernel__.Set_intf.Tree.t

val compare : t -> t -> Base.Int.t

type named = (t, Elt.comparator_witness) Core_kernel__.Set_intf.Tree.Named.t

include Core_kernel.Set_intf.Creators_and_accessors0
  with type ('a, 'b) set := ('a, 'b) Core_kernel__.Set_intf.Tree.t
  with type t := t
  with type tree := t
  with type elt := t
  with type named := named
  with type comparator_witness := Elt.comparator_witness

include Core_kernel.Set_intf.Accessors0
  with type t := t
  with type tree := t
  with type elt := t
  with type named := named
  with type comparator_witness := Elt.comparator_witness

val length : t -> int

val is_empty : t -> bool

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

val fold : t -> init:'accum -> f:('accum -> t -> 'accum) -> 'accum

val fold_result : 
  t ->
  init:'accum ->
  f:('accum -> t -> ('accum, 'e) Base__.Result.t) ->
  ('accum, 'e) Base__.Result.t

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

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

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

val sum : 
  (module Base__Container_intf.Summable with type t = 'sum) ->
  t ->
  f:(t -> 'sum) ->
  'sum

val find : t -> f:(t -> bool) -> t option

val find_map : t -> f:(t -> 'a option) -> 'a option

val to_list : t -> t list

val to_array : t -> t array

val invariants : t -> bool

val mem : t -> t -> bool

val add : t -> t -> t

val remove : t -> t -> t

val union : t -> t -> t

val inter : t -> t -> t

val diff : t -> t -> t

val symmetric_diff : t -> t -> (t, t) Base__.Either.t Base__.Sequence.t

val compare_direct : t -> t -> int

val equal : t -> t -> bool

val is_subset : t -> of_:t -> bool

val are_disjoint : t -> t -> bool

module Named : sig ... end

val fold_until : 
  t ->
  init:'b ->
  f:('b -> t -> ('b, 'final) Base__Set_intf.Continue_or_stop.t) ->
  finish:('b -> 'final) ->
  'final

val fold_right : t -> init:'b -> f:(t -> 'b -> 'b) -> 'b

val iter2 : 
  t ->
  t ->
  f:([ `Both of t * t | `Left of t | `Right of t ] -> unit) ->
  unit

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

val partition_tf : t -> f:(t -> bool) -> t * t

val elements : t -> t list

val min_elt : t -> t option

val min_elt_exn : t -> t

val max_elt : t -> t option

val max_elt_exn : t -> t

val choose : t -> t option

val choose_exn : t -> t

val split : t -> t -> t * t option * t

val group_by : t -> equiv:(t -> t -> bool) -> t list

val find_exn : t -> f:(t -> bool) -> t

val nth : t -> int -> t option

val remove_index : t -> int -> t

val to_tree : t -> t

val to_sequence : 
  ?order:[ `Decreasing | `Increasing ] ->
  ?greater_or_equal_to:t ->
  ?less_or_equal_to:t ->
  t ->
  t Base__.Sequence.t

val binary_search : 
  t ->
  compare:(t -> 'key -> int) ->
  [ `First_equal_to
  | `First_greater_than_or_equal_to
  | `First_strictly_greater_than
  | `Last_equal_to
  | `Last_less_than_or_equal_to
  | `Last_strictly_less_than ] ->
  'key ->
  t option

val binary_search_segmented : 
  t ->
  segment_of:(t -> [ `Left | `Right ]) ->
  [ `First_on_right | `Last_on_left ] ->
  t option

val merge_to_sequence : 
  ?order:[ `Decreasing | `Increasing ] ->
  ?greater_or_equal_to:t ->
  ?less_or_equal_to:t ->
  t ->
  t ->
  (t, t) Base__Set_intf.Merge_to_sequence_element.t Base__.Sequence.t

val to_map : 
  t ->
  f:(t -> 'data) ->
  (t, 'data, Elt.comparator_witness) Base.Map.t

val quickcheck_observer : 
  t Core_kernel.Quickcheck.Observer.t ->
  t Core_kernel.Quickcheck.Observer.t

val quickcheck_shrinker : 
  t Core_kernel.Quickcheck.Shrinker.t ->
  t Core_kernel.Quickcheck.Shrinker.t

include Core_kernel.Set_intf.Creators0
  with type t := t
  with type tree := t
  with type elt := t
  with type comparator_witness := Elt.comparator_witness
  with type ('a, 'b) set := ('a, 'b) Core_kernel__.Set_intf.Tree.t

val empty : t

val singleton : t -> t

val union_list : t list -> t

val of_list : t list -> t

val of_array : t array -> t

val of_sorted_array : t array -> t Base__.Or_error.t

val of_sorted_array_unchecked : t array -> t

val of_increasing_iterator_unchecked : len:int -> f:(int -> t) -> t

val stable_dedup_list : t list -> t list

val map : ('a, 'b) Core_kernel__.Set_intf.Tree.t -> f:('a -> t) -> t

val filter_map : 
  ('a, 'b) Core_kernel__.Set_intf.Tree.t ->
  f:('a -> t option) ->
  t

val of_tree : t -> t

val of_hash_set : t Core_kernel.Hash_set.t -> t

val of_hashtbl_keys : (t, _) Core_kernel.Hashtbl.t -> t

val of_map_keys : (t, _, Elt.comparator_witness) Base.Map.t -> t

val quickcheck_generator : 
  t Core_kernel.Quickcheck.Generator.t ->
  t Core_kernel.Quickcheck.Generator.t

module Provide_of_sexp (Elt : sig ... end) : sig ... end

val t_of_sexp : Sexplib0__.Sexp.t -> t

val sexp_of_t : t -> Sexplib0__.Sexp.t