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
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  - 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
    
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    OrderedType
    
    Proj
    
    A
    
    Map
    
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    Proj2
    
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    Projection
    
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    S
    
    Map
    
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    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
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    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

Intermediate representation of model on which sanity has been checked

type ('a, 'annoted) link =

| ANY_FREE
| LNK_VALUE of int * 'annoted
| LNK_FREE
| LNK_ANY
| LNK_SOME
| LNK_TYPE of 'a * 'a
(*
port * agent_type
*)

type switching =

| Linked of int
| Freed
| Maintained
| Erased

type rule_internal =

| I_ANY
| I_ANY_CHANGED of int
| I_ANY_ERASED
| I_VAL_CHANGED of int * int
| I_VAL_ERASED of int

type rule_agent = {

ra_type : int;
ra_erased : bool;
ra_ports : ((int, int * int) link Kappa_data_structures.Loc.annoted * switching) array;
ra_ints : rule_internal array;
ra_syntax : (((int, int * int) link Kappa_data_structures.Loc.annoted * switching) array * rule_internal array) option;

}

A representation of 'left-hand-side' agent that stores how everything is transformed. In an observable (a mixture in an alg_expr), everything is Maintained (represented by I_VAL_CHANGED (i,i) for internal states).

The field ra_syntax represents how the user describe the agent before compilation. Therefore, compil_of_ast in this module generates rule_agent where ra_syntax is Some (Array.copy ra_ports, Array.copy ra_ints).

type rule_mixture = rule_agent list

rule_mixture is the mixture description from the initial state of a rule

type rule = {

r_mix : rule_mixture;
(*
Initial mixture state
*)
r_created : Raw_mixture.t;
(*
Mixture state after rule is applied
*)
r_delta_tokens : ((rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted * int) list;
r_rate : (rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted;
r_un_rate : ((rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted * (rule_mixture, int) Alg_expr.e Kappa_data_structures.Loc.annoted option) option;
r_edit_style : bool;
(*
If rule was written in edit style, else it's rewrite style
*)

}

val agent_to_erased : Kappa_site_graphs.Signature.s -> rule_agent -> rule_agent

val to_erased : Kappa_site_graphs.Signature.s -> rule_mixture -> rule_mixture

val to_maintained : rule_mixture -> rule_mixture

val to_raw_mixture : 
  Kappa_site_graphs.Signature.s ->
  rule_mixture ->
  Raw_mixture.t

val copy_rule_agent : rule_agent -> rule_agent

val max_link_id : rule_mixture -> int

val raise_if_modification : Kappa_data_structures.Loc.t -> 'a option -> unit

val raise_several_internal_states : Kappa_data_structures.Loc.t -> 'a

val raise_not_enough_specified : 
  status:string ->
  side:string ->
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val raise_several_occurence_of_site : 
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val raise_counter_misused : 
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val raise_link_only_one_occurence : int -> Kappa_data_structures.Loc.t -> 'a

val raise_link_should_be_removed : 
  int ->
  string ->
  string Kappa_data_structures.Loc.annoted ->
  'a

val print_rule_mixture : 
  noCounters:bool ->
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  ltypes:bool ->
  Raw_mixture.t ->
  Format.formatter ->
  rule_mixture ->
  unit

val print_link : 
  ('a -> Format.formatter -> 'a -> unit) ->
  (Format.formatter -> 'a -> unit) ->
  (Format.formatter -> 'b -> unit) ->
  Format.formatter ->
  ('a, 'b) link ->
  unit

val link_to_json : 
  ('a -> 'a -> Yojson.Basic.t) ->
  ('a -> Yojson.Basic.t) ->
  ('b -> Yojson.Basic.t list) ->
  ('a, 'b) link ->
  Yojson.Basic.t

Fragile: the list MUST NOT be a singleton

val link_of_json : 
  ('a -> Yojson.Basic.t -> 'a) ->
  (Yojson.Basic.t -> 'a) ->
  (Yojson.Basic.t list -> 'b) ->
  Yojson.Basic.t ->
  ('a, 'b) link

val print_rates : 
  noCounters:bool ->
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  (Format.formatter -> int -> unit) ->
  (Format.formatter -> int -> unit) ->
  Format.formatter ->
  rule ->
  unit

val print_rule : 
  noCounters:bool ->
  full:bool ->
  Kappa_site_graphs.Signature.s ->
  Kappa_site_graphs.Counters_info.t ->
  (Format.formatter -> int -> unit) ->
  (Format.formatter -> int -> unit) ->
  Format.formatter ->
  rule ->
  unit

val rule_to_json : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  rule ->
  Yojson.Basic.t

val rule_of_json : filenames:string array -> Yojson.Basic.t -> rule