package kappa-library

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in-package search v0.2.0

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Use a connected component

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:
Library
Module
Module type
Parameter
Class
Class type

Domain to navigate in the graph

type link =

| UnSpec
| Free
| Link of int * int

type cc

type t = cc

type for domain points

type id

val debug_print_id : Format.formatter -> id -> unit

module ObsMap : sig ... end

Maps from patterns to something

module Env : sig ... end

module PreEnv : sig ... end

type work

Create a connected component

type of a PreEnv during a pattern construction

val empty_cc : Kappa_site_graphs.Signature.s -> cc

val begin_new : PreEnv.t -> work

Starts creation

val new_node : work -> int -> Kappa_site_graphs.Agent.t * work

new_node wk node_type

val new_link : 
  work ->
  (Kappa_site_graphs.Agent.t * int) ->
  (Kappa_site_graphs.Agent.t * int) ->
  work

new_link wk (node, site_id) (node', site_id')

val new_free : work -> (Kappa_site_graphs.Agent.t * int) -> work

val new_internal_state : 
  work ->
  (Kappa_site_graphs.Agent.t * int) ->
  int ->
  work

new_link_type work (node,site) type

val finish_new : 
  debug_mode:bool ->
  ?origin:Kappa_data_structures.Operator.rev_dep ->
  work ->
  PreEnv.t * Kappa_data_structures.Renaming.t * cc * id

Use a connected component

val compare_canonicals : id -> id -> int

val is_equal_canonicals : id -> id -> bool

val print_cc : 
  noCounters:bool ->
  ?dotnet:bool ->
  ?full_species:bool ->
  ?sigs:Kappa_site_graphs.Signature.s ->
  ?counters_info:Kappa_site_graphs.Counters_info.t ->
  ?cc_id:id ->
  with_id:bool ->
  Format.formatter ->
  t ->
  unit

val print_cc_as_id : 
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  Format.formatter ->
  t ->
  unit

val print : 
  noCounters:bool ->
  ?domain:Env.t ->
  with_id:bool ->
  Format.formatter ->
  id ->
  unit

print ~domain ?with_id:None form cc

val id_to_yojson : id -> Yojson.Basic.t

val id_of_yojson : Yojson.Basic.t -> id

val reconstruction_navigation : 
  t ->
  Kappa_site_graphs.Navigation.abstract Kappa_site_graphs.Navigation.t

val find_ty : cc -> int -> int

Abstraction leak, please do not use

val automorphisms : 
  debug_mode:bool ->
  t ->
  Kappa_data_structures.Renaming.t list

val embeddings_to_fully_specified : 
  debug_mode:bool ->
  Env.t ->
  id ->
  cc ->
  Kappa_data_structures.Renaming.t list

val size_of_cc : cc -> int

val fold_by_type : 
  (pos:int -> agent_type:int -> (link * int) array -> 'a -> 'a) ->
  cc ->
  'a ->
  'a

USE WITH CARE: Break some abstraction. The array must not be modified and internal state -1 means unspecified

val fold : (int -> (link * int) array -> 'acc -> 'acc) -> cc -> 'acc -> 'acc

USE WITH CARE: Break some abstraction. The array must not be modified and internal state -1 means unspecified

type sharing_level =

| No_sharing
| Compatible_patterns
| Max_sharing
(*
Heuristic to use on domain construction
*)

val write_sharing_level : Buffer.t -> sharing_level -> unit

Output a JSON value of type sharing_level.

val string_of_sharing_level : ?len:int -> sharing_level -> string

Serialize a value of type sharing_level into a JSON string.

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

val read_sharing_level : 
  Yojson.Safe.lexer_state ->
  Lexing.lexbuf ->
  sharing_level

Input JSON data of type sharing_level.

val sharing_level_of_string : string -> sharing_level

Deserialize JSON data of type sharing_level.

val finalize : 
  debug_mode:bool ->
  sharing:sharing_level ->
  PreEnv.t ->
  Contact_map.t ->
  Env.t * PreEnv.stat

val infs : debug_mode:bool -> Kappa_site_graphs.Signature.s -> t -> t -> t list

val matchings : 
  debug_mode:bool ->
  Kappa_site_graphs.Signature.s ->
  t ->
  t ->
  Kappa_data_structures.Renaming.t list

val merge_on_inf : 
  debug_mode:bool ->
  PreEnv.t ->
  Kappa_data_structures.Renaming.t ->
  t ->
  t ->
  t option * (t * int * t * int * int * bool) option

val length : t -> int

module Set : Kappa_data_structures.SetMap.Set with type elt = id

module Map : Kappa_data_structures.SetMap.Map with type elt = id

val counter_value_cc : 
  Kappa_site_graphs.Signature.s option ->
  Kappa_site_graphs.Counters_info.counter_sig ->
  cc ->
  (Kappa_data_structures.Mods.IntMap.elt * int) ->
  int