package kappa-library

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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:
Library
Module
Module type
Parameter
Class
Class type

Concrete graph implementation

type t

val empty : with_connected_components:bool -> t

val copy : t -> t

You'd better NOT use that on the state of a simulation

type stats = {

nb_agents : int;

}

val stats : t -> stats

val add_agent : ?id:int -> Signature.s -> int -> t -> int * t

add_agent ?id sigs agent_type graph

val add_free : int -> int -> t -> t

add_free agent_id site graph

val add_internal : int -> int -> int -> t -> t

add_internal agent_id site internal_state graph

val add_link : Agent.t -> int -> Agent.t -> int -> t -> t * (int * int) option

add_link ag1 s1 ag2 s2 t Some (i,j) as second returned element means cc j is now merged into cc i

val remove_agent : int -> t -> t

val remove_free : int -> int -> t -> t

val remove_internal : int -> int -> t -> int * t

val remove_link : int -> int -> int -> int -> t -> t * (int * int) option

Some (i,j) as second returned element means separate "new" cc j from cc i

val is_agent : Agent.t -> t -> bool

is_agent agent graph

val is_agent_id : int -> t -> bool

is_agent_id agent_id graph

val is_free : int -> int -> t -> bool

is_free agent_id site graph

val is_internal : int -> int -> int -> t -> bool

is_internal internal_state agent_id site graph

val link_exists : int -> int -> int -> int -> t -> bool

link_exists ag1_id site1 ag2_id site2 graph

val exists_fresh : int -> int -> int -> int -> t -> int option

exists_fresh ag1 site1 type_of_ag2 site2 graph

val link_destination : int -> int -> t -> (Agent.t * int) option

link_destination ag site graph

val get_internal : int -> int -> t -> int

get_internal ag site graph

val get_sites : int -> t -> int

val get_sort : int -> t -> int

val get_connected_component : int -> t -> int option

val in_same_connected_component : int -> int -> t -> bool

val iter_neighbors : (Agent.t -> unit) -> int -> t -> unit

iter_neighbors f ag graph calls function f on all direct neighbors of agent ag in graph.

val all_agents_where : 
  (Agent.t -> bool) ->
  t ->
  Kappa_data_structures.IntCollection.t

type path = ((Agent.t * int) * (Agent.t * int)) list

val empty_path : path

val singleton_path : Agent.t -> int -> Agent.t -> int -> path

val rev_path : path -> path

val print_path : ?sigs:Signature.s -> Format.formatter -> path -> unit

val is_valid_path : path -> t -> bool

val are_connected : 
  ?max_distance:int ->
  t ->
  Agent.t list ->
  Agent.t list ->
  path option

are_connected ?max_distance graph nodes_x nodes_y

val species : 
  debug_mode:bool ->
  Signature.s ->
  int ->
  t ->
  User_graph.connected_component

val build_snapshot : raw:bool -> Signature.s -> t -> Snapshot.t

val build_user_snapshot : 
  debug_mode:bool ->
  raw:bool ->
  Signature.s ->
  t ->
  (int * User_graph.connected_component) list

val debug_print : Format.formatter -> t -> unit