package kappa-library

You can search for identifiers within the package.

in-package search v0.2.0

kappa-library.generic
- Kappa_data_structures
  - Base64
  - Bigbuffer
  - Buffers
    
    Buffers
  - Cache
    
    Cache
    
    O
    
    OO
  - Circular_buffers
  - Color
  - Crc32
  - DynamicArray
    
    DynArray
    
    _
  - ExceptionDefn
  - Fifo
  - Fractions
  - GenArray
    
    GenArray
  - Hashed_list
    
    Hash
    
    Make
    
    A
  - Infinite_buffers
  - IntCollection
  - JsonUtil
  - LargeArray
  - List_util
    
    Infix
  - Loc
  - Mods
    
    CharSetMap
    
    Map
    
    Set
    
    DynArray
    
    Int2SetMap
    
    Map
    
    Set
    
    IntSetMap
    
    Map
    
    Set
    
    String2SetMap
    
    Map
    
    Set
    
    StringSetMap
    
    Map
    
    Set
  - NamedDecls
  - Nbr
  - Operator
    
    DepSet
  - Option_util
  - Pp
  - Pp_html
  - Random_tree
  - Renaming
  - Result_util
  - SetMap
    
    Make
    
    Map
    
    Ord
    
    Set
    
    Map
    
    OrderedType
    
    Proj
    
    A
    
    Map
    
    Set
    
    B
    
    Map
    
    Set
    
    Proj2
    
    A
    
    Map
    
    Set
    
    B
    
    Map
    
    Set
    
    C
    
    Map
    
    Set
    
    Projection
    
    Projection2
    
    S
    
    Map
    
    Set
    
    Set
  - Stop
  - Tools
  - ValMap
kappa-library.mixtures
- Kappa_site_graphs
  - Agent
    
    SetMap
    
    Map
    
    Set
  - Counters_info
  - Edges
  - Navigation
  - Signature
  - Snapshot
  - User_graph
kappa-library.runtime
- Kappa_runtime
  - Counter
    
    Efficiency
  - Data
  - Expr_interpreter
  - Fluxmap
  - Generic_rule_interpreter
    
    Make
    
    Instances
  - Instances
  - Instances_sig
    
    S
  - Replay
  - Resource_strings
  - Roots
  - Rule_interpreter
  - State_interpreter
  - Trace
    
    Simulation_info
kappa-library.terms
- Kappa_terms
  - Alg_expr
  - Alg_expr_extra
  - Configuration
  - Contact_map
  - Instantiation
  - Kappa_printer
  - LKappa
  - Matching
    
    Agent
  - Model
  - Pattern
    
    Env
    
    Map
    
    ObsMap
    
    PreEnv
    
    Set
  - Pattern_compiler
  - Pattern_decompiler
  - Primitives
    
    Transformation
  - Raw_mixture
kappa-library.utils
- Kappa_utils
  - Utils

Legend:
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Module
Module type
Parameter
Class
Class type

type snapshot = {

snapshot_event : int;
snapshot_time : float;
snapshot_agents : (int * Kappa_site_graphs.User_graph.connected_component) list;
snapshot_tokens : (string * Kappa_data_structures.Nbr.t) array;

}

type din_data = {

din_kind : Kappa_terms.Primitives.din_kind;
din_start : float;
din_hits : int array;
din_fluxs : float array array;

}

type din = {

din_rules : string array;
din_data : din_data;
din_end : float;

}

type file_line = {

file_line_name : string option;
file_line_text : string;

}

type t =

| DIN of string * din
| DeltaActivities of int * (int * (float * float)) list
| Plot of Kappa_data_structures.Nbr.t array
(*
Must have length >= 1 (at least T or E)
*)
| Print of file_line
| TraceStep of Trace.step
| Snapshot of string * snapshot
| Log of string
| Species of string * float * Kappa_site_graphs.User_graph.connected_component
| Warning of Kappa_data_structures.Loc.t option * Format.formatter -> unit

val print_snapshot : ?uuid:int -> Format.formatter -> snapshot -> unit

val print_dot_snapshot : ?uuid:int -> Format.formatter -> snapshot -> unit

val write_snapshot : Buffer.t -> snapshot -> unit

Output a JSON value of type snapshot.

val string_of_snapshot : ?len:int -> snapshot -> string

Serialize a value of type snapshot into a JSON string.

parameter len
specifies the initial length of the buffer used internally. Default: 1024.

val read_snapshot : Yojson.Safe.lexer_state -> Lexing.lexbuf -> snapshot

Input JSON data of type snapshot.

val snapshot_of_string : string -> snapshot

Deserialize JSON data of type snapshot.

val print_dot_din : ?uuid:int -> Format.formatter -> din -> unit

val print_html_din : Format.formatter -> din -> unit

val write_din : Buffer.t -> din -> unit

Output a JSON value of type din.

val string_of_din : ?len:int -> din -> string

Serialize a value of type din into a JSON string.

parameter len
specifies the initial length of the buffer used internally. Default: 1024.

val read_din : Yojson.Safe.lexer_state -> Lexing.lexbuf -> din

Input JSON data of type din.

val din_of_string : string -> din

Deserialize JSON data of type din.

type plot = {

plot_legend : string array;
plot_series : float option array list;

}

val add_plot_line : Kappa_data_structures.Nbr.t array -> plot -> plot

val init_plot : Kappa_terms.Model.t -> plot

val write_plot : Buffer.t -> plot -> unit

Output a JSON value of type plot.

val string_of_plot : ?len:int -> plot -> string

Serialize a value of type plot into a JSON string.

parameter len
specifies the initial length of the buffer used internally. Default: 1024.

val read_plot : Yojson.Safe.lexer_state -> Lexing.lexbuf -> plot

Input JSON data of type plot.

val plot_of_string : string -> plot

Deserialize JSON data of type plot.

val print_plot_legend : is_tsv:bool -> Format.formatter -> string array -> unit

val print_plot_line : 
  is_tsv:bool ->
  (Format.formatter -> 'a -> unit) ->
  Format.formatter ->
  'a array ->
  unit

val export_plot : is_tsv:bool -> plot -> string

val print_initial_inputs : 
  ?uuid:int ->
  Kappa_terms.Configuration.t ->
  Kappa_terms.Model.t ->
  Format.formatter ->
  (Kappa_terms.Primitives.alg_expr * Kappa_terms.Primitives.elementary_rule)
    list ->
  unit

val print_warning : 
  ?pos:Kappa_data_structures.Loc.t ->
  Format.formatter ->
  (Format.formatter -> unit) ->
  unit