Documentation · kappa-library 4.1.0

kappa-library

Public internals of the Kappa tool suite

Version

IN THIS PACKAGE

library kappa-library.generic
- module Kappa_generic_toolset
  - module Base64
  - module Bigbuffer
  - module Buffers
    
    module type Buffers
  - module Cache
    
    module Cache
    
    argument 1-OO
    
    module O
  - module Circular_buffers
  - module Color
  - module Crc32
  - module DynamicArray
    
    module DynArray
    
    argument 1-G
  - module ExceptionDefn
  - module Fifo
  - module Fractions
  - module GenArray
    
    module type GenArray
  - module Hashed_list
    
    module type Hash
    
    module Make
    
    argument 1-A
  - module Infinite_buffers
  - module IntCollection
  - module JsonUtil
  - module LargeArray
  - module List_util
    
    module Infix
  - module Locality
  - module Mods
    
    module CharSetMap
    
    module Map
    
    module Set
    
    module DynArray
    
    module Int2SetMap
    
    module Map
    
    module Set
    
    module IntSetMap
    
    module Map
    
    module Set
    
    module String2SetMap
    
    module Map
    
    module Set
    
    module StringSetMap
    
    module Map
    
    module Set
  - module NamedDecls
  - module Nbr
  - module Operator
    
    module DepSet
  - module Option_util
  - module Pp
  - module Pp_html
  - module Random_tree
  - module Renaming
  - module Result_util
  - module SetMap
    
    module Make
    
    argument 1-Ord
    
    module Map
    
    module Set
    
    module type Map
    
    module type OrderedType
    
    module Proj
    
    argument 1-A
    
    module Map
    
    module Set
    
    argument 2-B
    
    module Map
    
    module Set
    
    module Proj2
    
    argument 1-A
    
    module Map
    
    module Set
    
    argument 2-B
    
    module Map
    
    module Set
    
    argument 3-C
    
    module Map
    
    module Set
    
    module type Projection
    
    module type Projection2
    
    module type S
    
    module Map
    
    module Set
    
    module type Set
  - module Stop
  - module Tools
  - module ValMap
library kappa-library.mixtures
- module Kappa_mixtures
  - module Agent
    
    module SetMap
    
    module Map
    
    module Set
  - module Edges
  - module Navigation
  - module Signature
  - module Snapshot
  - module User_graph
library kappa-library.runtime
- module Kappa_runtime
  - module Counter
    
    module Efficiency
  - module Data
  - module Expr_interpreter
  - module Fluxmap
  - module Generic_rule_interpreter
    
    module Make
    
    argument 1-Instances
  - module Instances
  - module Instances_sig
    
    module type S
  - module Replay
  - module Resource_strings
  - module Roots
  - module Rule_interpreter
  - module State_interpreter
  - module Trace
    
    module Simulation_info
library kappa-library.terms
- module Kappa_terms
  - module Alg_expr
  - module Alg_expr_extra
  - module Configuration
  - module Contact_map
  - module Instantiation
  - module Kappa_printer
  - module LKappa
  - module Matching
    
    module Agent
  - module Model
  - module Pattern
    
    module Env
    
    module Map
    
    module ObsMap
    
    module PreEnv
    
    module Set
  - module Pattern_compiler
  - module Pattern_decompiler
  - module Primitives
    
    module Transformation
  - module Raw_mixture

Libraries

This package provides the following libraries (via dune):

kappa-library.generic

Documentation:

Kappa_generic_toolset.Base64 Base64 RFC4648 implementation.
Kappa_generic_toolset.Bigbuffer Extensible buffers.
Kappa_generic_toolset.Buffers
Kappa_generic_toolset.Cache * cache.ml * * a module for KaSim * Jérôme Feret, projet Abstraction, INRIA Paris-Rocquencourt * Jean Krivine, Université Paris-Diderot, CNRS * * KaSim * Jean Krivine, Université Paris-Diderot, CNRS * * Creation: 27/03/2012 * Last modification: 27/03/2012 * * * * It uses imperative styles to ensure compatibility with other modules * * Copyright 2011,2012 Institut National de Recherche en Informatique et * en Automatique. All rights reserved. This file is distributed * under the terms of the GNU Library General Public License
Kappa_generic_toolset.Circular_buffers
Kappa_generic_toolset.Color
Kappa_generic_toolset.Crc32
Kappa_generic_toolset.DynamicArray Array with dynamic size
Kappa_generic_toolset.ExceptionDefn
Kappa_generic_toolset.Fifo FIFO
Kappa_generic_toolset.Fractions
Kappa_generic_toolset.GenArray Signature of array only limited by max_int
Kappa_generic_toolset.Hashed_list
Kappa_generic_toolset.Infinite_buffers
Kappa_generic_toolset.IntCollection Imperative int set
Kappa_generic_toolset.JsonUtil Parsing utils
Kappa_generic_toolset.LargeArray Implementation of array only limited by max_int
Kappa_generic_toolset.List_util
Kappa_generic_toolset.Locality
Kappa_generic_toolset.Mods Datastructures' functors instantiation
Kappa_generic_toolset.NamedDecls Stores a bunch of stuff the user gave a name to
Kappa_generic_toolset.Nbr Kappa numbers (either float, int or int64) and operations on them
Kappa_generic_toolset.Operator Compiled algebraic expression
Kappa_generic_toolset.Option_util Utilities on option
Kappa_generic_toolset.Pp
Kappa_generic_toolset.Pp_html
Kappa_generic_toolset.Random_tree
Kappa_generic_toolset.Renaming Functions from a subset of nat to a subset of nat
Kappa_generic_toolset.Result_util
Kappa_generic_toolset.SetMap Our own implementattion of Set and Map
Kappa_generic_toolset.Stop
Kappa_generic_toolset.Tools Misc utilities
Kappa_generic_toolset.ValMap

Dependencies: yojson, result, logs, stdlib-shims, bigarray

kappa-library.mixtures

Documentation:

Kappa_mixtures.Agent A node of a site graph
Kappa_mixtures.Edges Concrete graph implementation
Kappa_mixtures.Navigation Pathes to explore a mixture
Kappa_mixtures.Signature Store definitions of agents
Kappa_mixtures.Snapshot
Kappa_mixtures.User_graph

Dependencies: kappa-library.generic

kappa-library.runtime

Documentation:

Kappa_runtime.Counter Simulation progress keeper
Kappa_runtime.Data
Kappa_runtime.Expr_interpreter Algebraic expression computation
Kappa_runtime.Fluxmap
Kappa_runtime.Generic_rule_interpreter Graph rewriting module
Kappa_runtime.Instances
Kappa_runtime.Instances_sig Collection of rectangular instances.
Kappa_runtime.Replay Utilities to make mixtures from traces
Kappa_runtime.Resource_strings
Kappa_runtime.Roots
Kappa_runtime.Rule_interpreter
Kappa_runtime.State_interpreter Event loop module
Kappa_runtime.Trace Trace of simulation

Dependencies: kappa-library.terms

kappa-library.terms

Documentation:

Kappa_terms.Alg_expr
Kappa_terms.Alg_expr_extra Primitives for handling rule rates when detecting symmetries
Kappa_terms.Configuration
Kappa_terms.Contact_map
Kappa_terms.Instantiation What users wrote when writing its rules
Kappa_terms.Kappa_printer Printers (user readable) of Kappa compiled units
Kappa_terms.LKappa Intermediate representation of model on wich sanity has been checked
Kappa_terms.Matching Injection from a pattern in the mixture
Kappa_terms.Model Compiled representation of a full Kappa model
Kappa_terms.Pattern Domain to navigate in the graph
Kappa_terms.Pattern_compiler Kappa pattern compiler
Kappa_terms.Pattern_decompiler
Kappa_terms.Primitives Compiled kappa model unit
Kappa_terms.Raw_mixture

Dependencies: kappa-library.mixtures