y_nelson 2.3.7 → 2.3.8

data/Object_model_of_YPetri_and_YNelson.lyx

@@ -1,3842 +0,0 @@
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-\index Index
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-\end_header
-
-\begin_body
-
-\begin_layout Title
-Object model of YNelson and YPetri
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-YNelson
-\family default
- and 
-\family typewriter
-YPetri
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\color blue
-YNelson
-\family default
-\color inherit
- is a Ruby library (gem) providing a domain model and a simulator of 
-\emph on
-\color green
-Nelson nets
-\emph default
-\color inherit
-.
- A 
-\emph on
-\color green
-Nelson net
-\emph default
-\color inherit
- is a cross between a 
-\emph on
-\color green
-Petri net
-\emph default
-\color inherit
-, and a 
-\emph on
-\color green
-ZZ structure
-\emph default
-\color inherit
-.
- For formal definition of the ZZ structure, see 
-\begin_inset CommandInset citation
-LatexCommand citet
-key "Dattolo2009fdz"
-
-\end_inset
-
-.
- 
-\family typewriter
-YNelson
-\family default
- has two major dependencies: 
-\family typewriter
-\color blue
-YPetri
-\family default
-\color inherit
- gem that provides Petri nets and 
-\family typewriter
-\color blue
-Yzz
-\family default
-\color inherit
- gem that provides ZZ structures.
- 
-\family typewriter
-YNelson
-\family default
- provides the same interface as 
-\family typewriter
-YPetri
-\family default
-, so this document is (except for 
-\family typewriter
-Yzz
-\family default
- features) applicable also to 
-\family typewriter
-YPetri
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-You should also take a look at the tutorial, 
-\begin_inset Quotes eld
-\end_inset
-
-Introduction_to_YNelson_and_YPetri
-\begin_inset Quotes erd
-\end_inset
-
-.
- However, the tutorial is a hands-on guide, while this document describes
- the abstraction of 
-\family typewriter
-YPetri
-\family default
- / 
-\family typewriter
-YNelson
-\family default
-.
- The described gems need Ruby 2.3 or newer and can be installed by typing
- 
-\family typewriter
-gem install y_nelson
-\family default
- in your command prompt.
- (The dependencies will install automatically.)
-\end_layout
-
-\begin_layout Part*
-Functional Petri nets
-\end_layout
-
-\begin_layout Standard
-Petri nets were described by C.
- A.
- Petri in the middle of 20th century.
- A Petri net can be used to represent various 
-\begin_inset Quotes eld
-\end_inset
-
-wiring diagrams
-\begin_inset Quotes erd
-\end_inset
-
- – production lines, railway networks, electronic circuits, computer architectur
-es, parallel execution diagrams, or chemical systems.
- In fact, Petri himself has designed Petri nets with chemical systems in
- mind.
-\end_layout
-
-\begin_layout Standard
-A Petri net consists of 
-\emph on
-\color green
-places
-\emph default
-\color inherit
-, 
-\emph on
-\color green
-transitions
-\emph default
-\color inherit
-, and 
-\emph on
-\color green
-arcs
-\emph default
-\color inherit
-.
- Places are typically drawn as circles, transitions as rectangles.
- Places and transitions are connected by arcs, drawn as lines or arrows.
- Places may contain 
-\emph on
-\color green
-tokens
-\emph default
-\color inherit
-.
- The amount of tokens in a place(s) is called 
-\emph on
-\color green
-marking
-\emph default
-\color inherit
-.
- When a transition operates (
-\emph on
-\color green
-fires
-\emph default
-\color inherit
-), tokens are added to or removed from its connected places.
- 
-\emph on
-\color green
-State
-\emph default
-\color inherit
- of a Petri net is fully expressed by the places' marking.
-\end_layout
-
-\begin_layout Standard
-Classical Petri nets are 
-\emph on
-\color green
-timeless
-\emph default
-\color inherit
-.
- In timeless Petri nets, firing of a transition is a discrete event, whose
- exact timing is not specified.
- Instead, conditions are specified, under which the transition is allowed
- or prohibited to fire (
-\emph on
-\color green
-enabled
-\emph default
-\color inherit
- or 
-\emph on
-\color green
-disabled
-\emph default
-\color inherit
-).
- Typically, transitions are enabled when their input arcs have sufficient
- amount of tokens left.
- However, different firing conditions may be specified.
- Timeless Petri nets are used to study concurrency – race conditions, network
- congestions, state reachability etc.
- Interaction with timeless Petri nets is called 
-\emph on
-\color green
-token game
-\emph default
-\color inherit
-.
-\end_layout
-
-\begin_layout Standard
-In 
-\emph on
-\color green
-timed Petri nets
-\emph default
-\color inherit
-, it is specified when (or how rapidly) firing of the transitions occurs.
- Timed nets are thus not interactive and can be autonomously 
-\emph on
-\color green
-executed
-\emph default
-\color inherit
- in time.
- Timed Petri nets actually represent a wiring diagram of a dynamic system.
- Under certain conditions, a set of differential equations (DE) describing
- the system can be extracted from this wiring diagram.
- Execution of a such Petri net is equivalent to numeric integration of its
- DE system.
-\family typewriter
-YPetri
-\family default
- object model
-\end_layout
-
-\begin_layout Standard
-Brief hands-on demonstration of the interface can be found in the document
- 
-\emph on
-Introduction to YNelson
-\emph default
-.
- The purpose of this chapter is to describe the Petri net object model of
- 
-\family typewriter
-YPetri
-\family default
- gem in more detail.
-\end_layout
-
-\begin_layout Part*
-Aspects of 
-\family typewriter
-YPetri
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri
-\family default
- has two main mutually intertwined concerns:
-\end_layout
-
-\begin_layout Enumerate
-To provide active object model of Petri nets.
-\end_layout
-
-\begin_layout Enumerate
-To provide simulation for the dynamic systems expressed as Petri nets.
-\end_layout
-
-\begin_layout Standard
-Correspondingly, 
-\family typewriter
-YPetri
-\family default
- has 2 aspects catering to its 2 concerns:
-\end_layout
-
-\begin_layout Enumerate
-Petri net aspect.
-\end_layout
-
-\begin_layout Enumerate
-Simulation aspect.
-\end_layout
-
-\begin_layout Standard
-Major classes of the Petri net aspect are 
-\family typewriter
-Place
-\family default
-, 
-\family typewriter
-Transition
-\family default
- and 
-\family typewriter
-Net
-\family default
-.
- Places have their own marking attribute, transitions know their connectivity,
- their functions, and they can be triggered to fire and modify marking of
- their connected places.
- 
-\family typewriter
-Net
-\family default
- is basically a specialized collection of places and transitions.
-\end_layout
-
-\begin_layout Standard
-Simulation aspect is catered for by 
-\family typewriter
-Simulation
-\family default
- class, representing a simulation run, and 
-\family typewriter
-Core
-\family default
- class representing a simulator – a machine that runs the calculations needed
- to perform the simulation steps.
-\end_layout
-
-\begin_layout Standard
-Workspace (
-\family typewriter
-World
-\family default
- class, where places, transitions and nets live), and manipulator (
-\family typewriter
-Agent
-\family default
- class that represents and assists the user) are straddled across both aspects
- of 
-\family typewriter
-YPetri
-\family default
-.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Place
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Place
-\family default
- class represents Petri net places.
- It includes 
-\family typewriter
-NameMagic
-\family default
- and is normally used as a parametrized subclass (PS) depending on 
-\family typewriter
-YPetri::World
-\family default
-.
- The key attribute of a place is its marking (variable 
-\family typewriter
-@marking
-\family default
-).
- Interface related to marking is:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#m
-\family default
-, alias 
-\family typewriter
-#value
-\family default
- – getter of 
-\family typewriter
-@marking
-\family default
- instance variable.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking
-\family default
- – convenience method that acts as 
-\family typewriter
-@marking
-\family default
- getter without arguments, but can be used to define guards if block is
- supplied to it.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking=
-\family default
-, alias 
-\family typewriter
-#value=
-\family default
-, alias 
-\family typewriter
-#m=
-\family default
- – setter of 
-\family typewriter
-@marking
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#add
-\family default
- and 
-\family typewriter
-#subtract
-\family default
- that change the value of 
-\family typewriter
-@marking
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#default_marking
-\family default
-, 
-\family typewriter
-#default_marking=
-\family default
- – getter and setter of place's default marking (
-\family typewriter
-@default_marking
-\family default
- variable).
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#has_default_marking?
-\family default
- – informs whether the place has default marking defined (
-\family typewriter
-@has_default_marking
-\family default
- variable).
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reset_marking
-\family default
- – sets 
-\family typewriter
-@marking
-\family default
- to the default value.
-\end_layout
-
-\begin_layout Standard
-Another important group of methods are those related to the place's connectivity
- – arcs.
- They are defined in the 
-\family typewriter
-YPetri::Place::Arcs
-\family default
- mixin included by 
-\family typewriter
-YPetri::Place
-\family default
-.
- In Petri net diagrams, arcs are the lines that connect places and transitions.
- In YPetri, there is no real 
-\begin_inset Quotes eld
-\end_inset
-
-arc
-\begin_inset Quotes erd
-\end_inset
-
- object.
- For places, 
-\family typewriter
-#arcs
-\family default
- method simply returns the connected transitions, and vice versa, for transition
-s, 
-\family typewriter
-#arcs
-\family default
- method returns connected places.
- Overview of the most important 
-\family typewriter
-Place
-\family default
- instance methods inherited from the 
-\family typewriter
-Arcs
-\family default
- mixin is here:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#upstream_arcs
-\family default
-, alias 
-\family typewriter
-#upstream_transitions
-\family default
- – getter of 
-\family typewriter
-@upstream_arcs
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#downstream_arcs
-\family default
-, alias 
-\family typewriter
-#downstream_transitions
-\family default
- – getter of 
-\family typewriter
-@downstream_arcs
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#arcs
-\family default
- – a union of upstream transitions and downstream transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#aa
-\family default
- – names of the connected transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#precedents
-\family default
- – precedents in the spreadsheet sense.
- Places whose marking directly influences firing of the upstream transitions
- of this place.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#dependents
-\family default
- – dependents in the spreadsheet sense.
- Places whose marking is changed by firing of the downstream transitions
- of this place.
-\end_layout
-
-\begin_layout Standard
-For the remaining methods, see the class documentation.
- Place can also have guards, statements that validate the marking and limit
- it to only certain values.
- At the moment, guards are not fully handled by the 
-\family typewriter
-Simulation
-\family default
- class.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Transition
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Transition
-\family default
- class represents Petri net transitions.
- They are 
-\begin_inset Quotes eld
-\end_inset
-
-functional
-\begin_inset Quotes erd
-\end_inset
-
- in the sense that they may have mathematical functions attached to them,
- that govern their firing according to the current marking of the Petri
- net places.
- (Term 
-\begin_inset Quotes eld
-\end_inset
-
-functional
-\begin_inset Quotes erd
-\end_inset
-
- has also been used in other meanings in conjunction with Petri nets.) 
-\family typewriter
-YPetri::Transition
-\family default
- class utilizes 
-\family typewriter
-NameMagic
-\family default
- mixin.
- 
-\family typewriter
-YPetri::Transition
-\family default
- class is normally used as a parametrized subclass (PS) depending on 
-\family typewriter
-YPetri::World
-\family default
-.
- The most prominent attribute of a 
-\family typewriter
-Transition
-\family default
- instance is its function.
- There are 4 basic types of transitions in 
-\family typewriter
-YPetri
-\family default
-:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-ts
-\family default
- – timeless nonstoichiometric
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-tS
-\family default
- – timeless stoichiometric
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-Ts
-\family default
- – timed nonstoichiometric
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-TS
-\family default
- – timed stoichiometric
-\end_layout
-
-\begin_layout Standard
-They arise by combining 2 basic qualities:
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-timedness
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-stoichiometricity
-\end_layout
-
-\begin_layout Standard
-You can find more information in the documentation of 
-\family typewriter
-YPetri::Transition
-\family default
- class.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Net
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Net
-\family default
- class represents functional Petri nets.
- It includes 
-\family typewriter
-NameMagic
-\family default
- and is normally used as a PS depending on 
-\family typewriter
-YPetri::World
-\family default
-.
- It is basically a specialized collection of 
-\family typewriter
-Place
-\family default
- instances and 
-\family typewriter
-Transition
-\family default
- instances.
- A transition may only be included in a net if all the places connected
- to it belong to the same net.
- 
-\family typewriter
-Net
-\family default
- instances own 2 parametrized subclasses:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#State
-\family default
- – getter of 
-\family typewriter
-@State
-\family default
-, a PS of 
-\family typewriter
-YPetri::Net::State
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Simulation
-\family default
- – getter of 
-\family typewriter
-@Simulation
-\family default
-, a PS of 
-\family typewriter
-YPetri::Simulation
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-Important instance methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#include_place
-\family default
- – adds a place to the net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#include_transition
-\family default
- – adds a transition to the net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#exclude_place
-\family default
- – removes a place from the net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#exclude_transition
-\family default
- – removes a transition from the net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#include_net
-\family default
- alias 
-\family typewriter
-#merge!
-\family default
- – includes another net in this net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#exclude_net
-\family default
- – removes the elements of another net from this net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#<<
-\family default
- – includes an element in the net
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#+
-\family default
- – returns a new net containing the union of the operands' elements
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#-
-\family default
- – returns a new net containing the elements of the receiver minus the operand
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#functional?
-\family default
- – inquirer whether the net is functional
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#timed?
-\family default
- – inquirer whether the net is timed
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#simulation
-\family default
- – constructor of a new simulation of this net
-\end_layout
-
-\begin_layout Standard
-A 
-\family typewriter
-Net
-\family default
- instance has its own state, and can be asked about place marking, transiton
- flux etc.
- It is also capable of drawing a diagram with Graphviz, using 
-\family typewriter
-#visualize
-\family default
- method.
- For full listing of methods, see the class documentation.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-World
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::World
-\family default
- is the space where places, transitions and nets live.
- Originally, this class was named 
-\family typewriter
-Workspace
-\family default
-, but 
-\family typewriter
-World
-\family default
- is shorter.
- Owns PS of 
-\family typewriter
-Place
-\family default
-, 
-\family typewriter
-Transition
-\family default
- and 
-\family typewriter
-Net
-\family default
-, stored respectively in 
-\family typewriter
-@Place
-\family default
-, 
-\family typewriter
-@Transition
-\family default
- and 
-\family typewriter
-@Net
-\family default
- instance variables.
- Their instances can be constructed with:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Place
-\family default
- – constructor of instances of 
-\family typewriter
-Place
-\family default
- PS.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Transition
-\family default
- – constructor of instances of 
-\family typewriter
-Transition
-\family default
- PS.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Net
-\family default
- constructor – constructor of instances of 
-\family typewriter
-Net
-\family default
- PS.
-\end_layout
-
-\begin_layout Standard
-World assets are divided into two mixins: 
-\family typewriter
-YPetri::World::PetriNetAspect
-\family default
- and 
-\family typewriter
-YPetri::World::SimulationAspect
-\family default
-.
- Important instance methods of PetriNetAspect are:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#place
-\family default
- – 
-\family typewriter
-Place
-\family default
- PS instance finder.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#transition
-\family default
- – 
-\family typewriter
-Transition
-\family default
- PS instance finder.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#net
-\family default
- – 
-\family typewriter
-Net
-\family default
- PS instance finder.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#places
-\family default
- – returns all 
-\family typewriter
-Place
-\family default
- PS instances.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#transitions
-\family default
- – returns all 
-\family typewriter
-Transition
-\family default
- PS instances.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#nets
-\family default
- – returns all 
-\family typewriter
-Net
-\family default
- PS instances.
-\end_layout
-
-\begin_layout Standard
-Important instance methods of SimulationAspect are:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#new_simulation
-\family default
- – constructor of simulations.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#simulation
-\family default
- – 
-\family typewriter
-Simulation
-\family default
- instance finder.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#simulations
-\family default
- – getter of 
-\family typewriter
-@simulations
-\family default
-, a hash of simulation instances and their settings.
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-World
-\family default
- instance has also 3 instance variables useful for simulations, 
-\family typewriter
-@clamp_collections
-\family default
-, 
-\family typewriter
-@initial_marking_collections
-\family default
- and 
-\family typewriter
-@simulation_settings_collections
-\family default
-.
- Each simulation requires an initial marking collection, a clamp collection,
- and a hash of simulation settings.
- In a world, these collections / settings can be named and stored in the
- above mentioned instance variables for later use in simulations.
- See the class documentation for more details and the accessor methods of
- these instance variables.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Simulation
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-While 
-\family typewriter
-YPetri
-\family default
- places have their own marking and the transitions make it possible to play
- the token game interactively, for many reasons, it is desirable to be able
- to execute Petri nets automatically.
- 
-\family typewriter
-YPetri::Simulation
-\family default
- class represents such simulations.
- 
-\family typewriter
-Simulation
-\family default
- instances do not operate directly on the Petri nets from which they were
- constructed.
- Instead, they form a representation (
-\begin_inset Quotes eld
-\end_inset
-
-mental image
-\begin_inset Quotes erd
-\end_inset
-
-) of the places and transitions of the underlying net.
- 
-\family typewriter
-Simulation
-\family default
- instances do not change the state owned by the underlying net.
- Instead, they have their own marking vector, which they modify using a
- chosen simulation method in the way that simulates firing of the transitions.
- A simulation owns multiple parametrized subclasses:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Place
-\family default
- – getter of 
-\family typewriter
-@Place
-\family default
-, a PS of 
-\family typewriter
-Simulation::PlaceRepresentation
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Transition
-\family default
- – getter of 
-\family typewriter
-@Transition, a 
-\family default
-PS of 
-\family typewriter
-Simulation::TransitionRepresentation
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Places
-\family default
- – getter of 
-\family typewriter
-@Places
-\family default
-, a PS of 
-\family typewriter
-Simulation::Places
-\family default
-, representing a collection of place representations.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Transitions
-\family default
- – getter of 
-\family typewriter
-@Transitions
-\family default
-, a PS of 
-\family typewriter
-Simulation::Transitions
-\family default
-, representing a collection of place representations.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Elements
-\family default
- – getter of 
-\family typewriter
-@Places
-\family default
-, a PS of 
-\family typewriter
-Simulation::Elements
-\family default
-, representing a collection of element (either place or transition) representati
-ons.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#PlaceMapping
-\family default
- – getter of 
-\family typewriter
-@PlaceMapping
-\family default
-, a PS of 
-\family typewriter
-Simulation::PlaceMapping
-\family default
-, a specialized 
-\family typewriter
-Hash
-\family default
- that maps the simulation's places to a set of some values.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#InitialMarking
-\family default
- – getter of 
-\family typewriter
-@InitialMarking
-\family default
-, a PS of 
-\family typewriter
-Simulation::InitialMarking
-\family default
-, which in turn is a subclass of 
-\family typewriter
-PlaceMapping
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#MarkingClamps
-\family default
- – getter of 
-\family typewriter
-@MarkingClamps
-\family default
-, a PS of 
-\family typewriter
-Simulation::MarkingClamps
-\family default
-, which in turn is a subclass of 
-\family typewriter
-PlaceMapping
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-Simulation can be of two types: Timed or timeless.
- These two types are defined in two mixins, 
-\family typewriter
-Simulation::Timed
-\family default
- and 
-\family typewriter
-Simulation::Timeless
-\family default
-, with which the simulation instance is conditionally extended during its
- initialization, depending on its type.
- Simulation has a number of specialized instance methods defined in several
- mixins located inside the 
-\family typewriter
-Simulation
-\family default
- namespace (
-\family typewriter
-Places::Access
-\family default
-, 
-\family typewriter
-Transitions::Access
-\family default
-, 
-\family typewriter
-Elements::Access
-\family default
-, 
-\family typewriter
-InitialMarking::Access
-\family default
-, 
-\family typewriter
-MarkingClamps::Access
-\family default
-, 
-\family typewriter
-MarkingVector::Access
-\family default
-).
- You can find their complete listing in the class documentation.
- Some of the instance methods are:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reset!
-\family default
- – resets the simulation.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#run!
-\family default
- – runs the simulation.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#run_upto
-\family default
- – runs the simulation to a given time (same can be achieved by 
-\begin_inset Quotes eld
-\end_inset
-
-
-\family typewriter
-run( upto: ...
- )
-\family default
-
-\begin_inset Quotes erd
-\end_inset
-
-).
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#step!
-\family default
- – steps the simulation.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#settings
-\family default
- – returns all the settings for this simulation.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#core
-\family default
- – simulator currently in use.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#recorder
-\family default
- – recorder instance currently in use.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#tS_SM
-\family default
- – stoichiometric matrix for tS transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#TS_SM
-\family default
- – stoichiometric matrix for TS transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#dup
-\family default
- – duplicate of the receiver simulation, with the possibility to change
- time and/or other simulation settings.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::Places::Access
-\family default
-:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#include_place?
-\family default
- – inquirer whether the simulation includes a specified place.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#p
-\family default
- – net's place identified by the argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Pp
-\family default
- – net's places, expects single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#pp
-\family default
- – net's places, arbitrary number of arguments.
- If called without arguments, returns all the net's places.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Free_pp
-\family default
-, alias 
-\family typewriter
-#free_Pp
-\family default
- – net's free places, single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#free_pp
-\family default
- – net's free places, arbitrary number of arguments.
- If called without arguments, returns all of them.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Clamped_pp
-\family default
-, alias 
-\family typewriter
-#clamped_Pp
-\family default
- – net's free places, single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#clamped_pp
-\family default
- – net's free places, arbitrary number of arguments.
- If called without arguments, returns all of them.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::Transitions::Access
-\family default
-:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#include_transition?
-\family default
- – inquirer whether the simulation includes a specified place.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#t
-\family default
- – net's transition identified by the argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Tt
-\family default
- – net's transitions, expects array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#tt
-\family default
- – net's transitions, arbitrary number of arguments.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#ts_Tt
-\family default
-, 
-\family typewriter
-#tS_Tt
-\family default
-, 
-\family typewriter
-#Ts_Tt
-\family default
-, 
-\family typewriter
-#TS_Tt
-\family default
-, 
-\family typewriter
-#A_Tt
-\family default
- etc.
- – net's transitions of the specified type.
- As signified by capitalized 
-\begin_inset Quotes eld
-\end_inset
-
-
-\family typewriter
-Tt
-\family default
-
-\begin_inset Quotes erd
-\end_inset
-
-, these methods expects a single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#ts_tt
-\family default
-, 
-\family typewriter
-#tS_tt
-\family default
-, 
-\family typewriter
-#Ts_tt
-\family default
-, 
-\family typewriter
-#TS_tt
-\family default
-, 
-\family typewriter
-#A_tt
-\family default
- etc.
- – versions of tnet's transitions of the specified type.
- As signified by capitalized 
-\begin_inset Quotes eld
-\end_inset
-
-
-\family typewriter
-Tt
-\family default
-
-\begin_inset Quotes erd
-\end_inset
-
-, these methods expects a single array argument.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::Elements::Access
-\family default
- (word 
-\begin_inset Quotes eld
-\end_inset
-
-element
-\begin_inset Quotes erd
-\end_inset
-
- simply stands for etiher place, or transition):
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#include?
-\family default
- – inquirer whether the simulation includes a specified place or transition.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#e
-\family default
- – net's element identified by the argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Ee
-\family default
- – net's elements identified by a single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#ee
-\family default
- – net's elements, arbitrary number of arguments.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::InitialMarking::Access
-\family default
-:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Initial_markings
-\family default
-, alias 
-\family typewriter
-#initial_Markings
-\family default
- – initial markings of given 
-\emph on
-free
-\emph default
- places, single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#initial_markings
-\family default
-, alias 
-\family typewriter
-#initial_marking
-\family default
- – initial markings, arbitrary number of arguments identifying free places.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Im
-\family default
- – starting markings of an array of 
-\emph on
-any
-\emph default
- (not just free) places, as they appear right after reset.
- Expects a single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#im
-\family default
- – starting markings of any places, arbitrary number of arguments.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::MarkingClamps::Access
-\family default
-:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Marking_clamps
-\family default
-, alias 
-\family typewriter
-#marking_Clamps
-\family default
- – marking clamp values of given 
-\emph on
-clamped
-\emph default
- places, single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking_clamps
-\family default
- – initial markings, arbitrary number of arguments.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking_clamp
-\family default
- – expects a single clamped place, returns its marking clamp.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::MarkingVector::Access
-\family default
-:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#M_vector
-\family default
- alias 
-\family typewriter
-#m_Vector
-\family default
- – marking of the selected places returned as a column vector.
- Expects a single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#state
-\family default
- – getter of the simulation's state vector (
-\family typewriter
-@m_vector
-\family default
- instance variable).
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#m_vector
-\family default
- – marking of the selected places returned as a column vector, any number
- of arguments.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#M
-\family default
-, 
-\family typewriter
-#m
-\family default
- – array-returning varieties of 
-\family typewriter
-#M_vector
-\family default
- and 
-\family typewriter
-#m
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#p_M
-\family default
- (alias 
-\family typewriter
-#P_m
-\family default
-), 
-\family typewriter
-#p_m
-\family default
- – hash-returning varieties of 
-\family typewriter
-#M_vector
-\family default
- and 
-\family typewriter
-#m
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Pm
-\family default
-, 
-\family typewriter
-#pm
-\family default
- – pretty printing varieties of 
-\family typewriter
-#M_vector
-\family default
- and 
-\family typewriter
-#m
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::Timed
-\family default
- and 
-\family typewriter
-Simulation::Timeless
-\family default
- mixins:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#timed?
-\family default
- – inquirer whether the simulation is timed
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Recorder
-\family default
- – getter of 
-\family typewriter
-@Recorder
-\family default
-, a PS of 
-\family typewriter
-Petri::Simulation::Recorder
-\family default
-, an object that performs sampling and recording during simulation.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Core
-\family default
- – getter of 
-\family typewriter
-@Core
-\family default
-, a PS of 
-\family typewriter
-YPetri::Core
-\family default
-, a machine abstraction class.
-\end_layout
-
-\begin_layout Standard
-Defined in 
-\family typewriter
-Simulation::Timed
-\family default
- mixin:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#time
-\family default
- – current simulation time
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#initial_time
-\family default
- – initial time of the simulation
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#target_time
-\family default
- – target time of the simulation (used when 
-\family typewriter
-#run!
-\family default
- is called without arguments)
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#time_range
-\family default
- – range-returning alternative for 
-\family typewriter
-#initial_time
-\family default
- and 
-\family typewriter
-#target_time
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#step
-\family default
-, 
-\family typewriter
-#step=
-\family default
- – getter and setter of the simulation step size
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#default_sampling
-\family default
- – sampling period for the simulation
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Fluxes
-\family default
- – takes a single array of TS transitions and returns their fluxes under
- current marking.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#fluxes
-\family default
-, alias 
-\family typewriter
-#flux
-\family default
- – like 
-\family typewriter
-#Fluxes
-\family default
-, but takes an arbitrary number of arguments.
- If no arguments are supplied, returns all of them.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#T_fluxes
-\family default
- (alias 
-\family typewriter
-#t_Fluxes
-\family default
-), 
-\family typewriter
-#t_fluxes
-\family default
- (alias 
-\family typewriter
-#t_flux
-\family default
-) – hash-returning varieties of 
-\family typewriter
-#Fluxes
-\family default
- and 
-\family typewriter
-#fluxes
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#pflux
-\family default
- – pretty-printing variety of 
-\family typewriter
-#t_flux
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-The above list of methods is not exhaustive.
- For full list of methods and their documentation, see the documentation
- of the 
-\family typewriter
-Simulation
-\family default
- class.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Simulation::Recorder
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Simulation::Recorder 
-\family default
-is a class used exclusively as a PS dependent on 
-\family typewriter
-YPetri::Simulation
-\family default
- instances.
- Its has tow key attributes:
-\end_layout
-
-\begin_layout Enumerate
-
-\family typewriter
-#features
-\family default
- – getter of 
-\family typewriter
-@features
-\family default
-, containing the feature set to be recorded.
- Its class is a PS of 
-\family typewriter
-Net::State::Features
-\family default
-.
- It can be specified explicitly upon initialization or via 
-\family typewriter
-#reset!
-\family default
- method.
- By default, markings of the free places are used.
-\end_layout
-
-\begin_layout Enumerate
-
-\family typewriter
-#recording
-\family default
- – getter of 
-\family typewriter
-@recording
-\family default
-, containing the recording itself.
- Its class is a PS of 
-\family typewriter
-Net::DataSet
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-In the course of simulation, the recorder performs sampling: Upon occurence
- of certain events, it records the feature set and stores it in the 
-\family typewriter
-@recording
-\family default
- object.
- For timed simulations, events are typically specified by time (
-\family typewriter
-@next_time
-\family default
- variable).
- Timeless simulations are not handled in the current version of 
-\family typewriter
-YPetri
-\family default
-, but it can already be said that events will be specified as conditions
- defined on the marking vector (
-\family typewriter
-@next_event
-\family default
- variable).
- Recorder's checking for whether the sampling condition is fulfilled is
- triggered by the 
-\family typewriter
-:alert!
-\family default
- message.
- 
-\family typewriter
-Recorder.new
-\family default
- constructor takes the following named arguments:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-features:
-\family default
- the feature set to record.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-recording:
-\family default
- option to plug a pre-constructed dataset to the recorder.
-\end_layout
-
-\begin_layout Standard
-In timed simulations, 
-\family typewriter
-Recorder.new
-\family default
- also accepts:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-sampling:
-\family default
- sampling period
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-next_time:
-\family default
- the next sampling time
-\end_layout
-
-\begin_layout Standard
-Important instance methods of 
-\family typewriter
-Recorder
-\family default
- are:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#new_recording
-\family default
- – constructs a new recording dependent on 
-\family typewriter
-@features
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reset!
-\family default
- – resets 
-\family typewriter
-@recording
-\family default
- and optionally changes 
-\family typewriter
-@features
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#alert!
-\family default
- – recorder expects this message whenever the system state changes.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#sample!
-\family default
- – private method that performs sampling
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Core
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Core
-\family default
- class is the abstraction for the simulator machine.
- Originally, it was named 
-\family typewriter
-Simulator
-\family default
-, but 
-\family typewriter
-Core
-\family default
- is shorter.
- When a 
-\family typewriter
-Simulation
-\family default
- instance wants to proceed in time to a next state, it relies on a 
-\family typewriter
-Core
-\family default
- instance to perform the computation.
- 
-\family typewriter
-Core
-\family default
- was separated from 
-\family typewriter
-Simulation
-\family default
- for the purpose of facilitating future use of different machines to run
- the simulation.
- At the moment, plain Ruby is used to compute the simulation steps.
- 
-\family typewriter
-Core
-\family default
- instance is generally not directly controlled by the user.
-
-\family typewriter
- Core
-\family default
- provides certain some basic interface, on which its mixins defining the
- different simulation methods rely:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#flux_vector
-\family default
- – flux vector for the nets with only TS transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#flux_vector_TS
-\family default
- – for mixed nets, returns flux vector for only TS transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#firing_vector_tS
-\family default
- – firing vector of tS transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#delta_tS
-\family default
- – delta state caused by tS transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#delta_ts
-\family default
- – delta state caused by ts transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#gradient
-\family default
- – total system gradient for free places.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#gradient_Ts
-\family default
- – gradient contribution by Ts transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#gradient_TS
-\family default
- – gradient contribution by TS transitions.
-\end_layout
-
-\begin_layout Standard
-For the purpose of controlling the marking vector, 
-\family typewriter
-Core
-\family default
- provides 2 instance methods:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#assignment_transitions_all_fire!
-\family default
- – fires all A (assignment) transitions.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#increment_marking_vector
-\family default
- – expects a delta vector of the same size as the marking vector as its
- singe argument, and increments the marking vector by it.
-\end_layout
-
-\begin_layout Standard
-Simulation method mixins take flux, gradient, delta etc., and based on them,
- compute the overall delta state, change the marking vector and fire assignment
- transitions as defined by the simulation method, alerting the recorder
- when the state changes.
- At the moment, simulation methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-:euler
-\family default
- – 1st order method for nets with only T (timed) transitions.
- Mixin: 
-\family typewriter
-Core::Timed::Euler
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-:pseudo_euler
-\family default
- – Euler method adaptation for nets with timeless transitions.
- Mixin: 
-\family typewriter
-Core::Timed::PseudoEuler
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-:gillespie
-\family default
- – For nets with only T transitions.
- Mixin: 
-\family typewriter
-Core::Timed::Gillespie
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-:runge_kutta
-\family default
- – 5th order method for nets with only T transitions.
- Mixin: 
-\family typewriter
-Core::Timed::RungeKutta
-\family default
-.
- (
-\emph on
-Not working at the moment!
-\emph default
-)
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-State
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-The state of a Petri net is entirely given by marking of its places.
- 
-\family typewriter
-Simulation
-\family default
- instances maintain their own marking vector holding the net state, but
- the net instance also has it's own state class, a PS of 
-\family typewriter
-YPetri::Net::State
-\family default
- < 
-\family typewriter
-Array
-\family default
-.
- 
-\family typewriter
-State
-\family default
- class is thus commonly used as a PS dependent on a 
-\family typewriter
-Net
-\family default
- instance, whose array positions correspond to the net's places.
- This net is available as a public class method on the 
-\family typewriter
-State
-\family default
- PS:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#net
-\family default
- – returns the net on which this State PS depends.
-\end_layout
-
-\begin_layout Standard
-Each such 
-\family typewriter
-State
-\family default
- PS in turn owns 2 dependent parametrized subclasses:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Feature
-\family default
- – getter of 
-\family typewriter
-@Feature
-\family default
-, containing a PS of 
-\family typewriter
-State::Feature
-\family default
-.
- When called with arguments, acts as alias of 
-\family typewriter
-#feature
-\family default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Features
-\family default
- – getter of 
-\family typewriter
-@Features
-\family default
-, containing a PS of 
-\family typewriter
-State::Features
-\family default
-.
- When called with a single array argument, this message acts as a feature
- set constructor / validator.
-\end_layout
-
-\begin_layout Standard
-Other public class methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#feature
-\family default
- – 
-\family typewriter
-@Feature
-\family default
- instance identifier.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#features
-\family default
- – 
-\family typewriter
-@Features
-\family default
- instance constructor.
- (See the class documentation for its full description.)
-\end_layout
-
-\begin_layout Standard
-Instance methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#to_record
-\family default
- – given clamped places, it returns a 
-\family typewriter
-Record
-\family default
- instance containing the marking of the free places.
- If no set of clamped places is supplied, it is considered empty.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking
-\family default
- – returns the marking of a single given place in this 
-\family typewriter
-State
-\family default
- instance.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#markings
-\family default
- – expects an arbitrary number of places, returns a plain array of their
- markings.
- If no arguments are given, returns all of them.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Feature
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-A feature defines a measurement which can be performed on a net in some
- state to extract the feature's value.
- In 
-\family typewriter
-YPetri
-\family default
-, 
-\family typewriter
-Net::State::Feature
-\family default
- class is used as a PS dependent on a 
-\family typewriter
-State
-\family default
- PS (not on a 
-\family typewriter
-State
-\family default
- instance):
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#State
-\family default
- – the 
-\family typewriter
-State
-\family default
- PS by which this 
-\family typewriter
-Feature
-\family default
- PS was parametrized.
-\end_layout
-
-\begin_layout Standard
-In the present implementation, this class serves as a mother class for more
- specialized feature classes: 
-\family typewriter
-Marking
-\family default
-, 
-\family typewriter
-Firing
-\family default
-, 
-\family typewriter
-Flux
-\family default
-, 
-\family typewriter
-Gradient
-\family default
-, 
-\family typewriter
-Delta
-\family default
- and 
-\family typewriter
-Assignment
-\family default
-.
- These are defined as 
-\family typewriter
-Feature
-\family default
- subclasses on the namespace of 
-\family typewriter
-Feature
-\family default
- itself, but at the same time, a PS of each of them is owned by the Feature
- PS:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Marking
-\family default
-, 
-\family typewriter
-#Firing
-\family default
-, 
-\family typewriter
-#Flux
-\family default
-, 
-\family typewriter
-#Gradient
-\family default
-, 
-\family typewriter
-#Delta
-\family default
-, 
-\family typewriter
-#Assignment
-\family default
- – these public class methods defined on a PS of Feature returns the dependent
- parametrized subclasses for the classes of the same name (
-\family typewriter
-Feature::Marking
-\family default
-, 
-\family typewriter
-Feature::Firing
-\family default
-, etc.)
-\end_layout
-
-\begin_layout Standard
-Instance methods are defined inside these specialized feature subclasses,
- such as:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#extract_from
-\family default
- – extracts the receiver feature from the target object, returning the feature's
- value.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#type
-\family default
- – feature type
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#label
-\family default
- – feature label (for use in graphics etc.)
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Features
-\family default
- class – feature set
-\end_layout
-
-\begin_layout Standard
-A collection of features is called a feature set.
- Measurement performed for a particular feature set results in a record.
- In 
-\family typewriter
-YPetri
-\family default
-, 
-\family typewriter
-Net::State::Features
-\family default
- is a subclass of 
-\family typewriter
-Array
-\family default
-, representing an array of features.
- Originally, it was named 
-\family typewriter
-FeatureSet
-\family default
-, but 
-\family typewriter
-Features
-\family default
- is shorter.
- It is used as a PS dependent on a 
-\family typewriter
-State
-\family default
- PS (
-\emph on
-not
-\emph default
- on a 
-\family typewriter
-State
-\family default
- instance).
- It's owning 
-\family typewriter
-State
-\family default
- PS can be accessed via 
-\family typewriter
-#State
-\family default
- class method.
- Such 
-\family typewriter
-Features
-\family default
- PS in turn owns subclasses of 
-\family typewriter
-Net::State::Features::Record
-\family default
- and 
-\family typewriter
-Net::Dataset
-\family default
-, which can be accessed via 
-\family typewriter
-#Record
-\family default
- and 
-\family typewriter
-#Dataset
-\family default
- class methods.
- Other class methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Marking
-\family default
-, 
-\family typewriter
-#Firing
-\family default
-, 
-\family typewriter
-#Flux
-\family default
-, 
-\family typewriter
-#Assignment
-\family default
- – constructors of a set of marking features, accepting single array argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking
-\family default
-, 
-\family typewriter
-#firing
-\family default
-, 
-\family typewriter
-#flux
-\family default
-, 
-\family typewriter
-#assignment
-\family default
- – versions of the above constructors, that accept any number of arguments,
- and return full corresponding feature sets if no arguments are given.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Gradient
-\family default
- – constructor of a set of gradient features, accepting an array and an
- optional :transitions named argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#gradient
-\family default
- – version of the above constructor accepting any number of ordered arguments,
- and returning full gradient feature set if no ordered arguments are given.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Delta
-\family default
- – constructor of a set of delta features, accepting an array and an optional
- :transitions named argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#delta
-\family default
- – version of the above constructor accepting any number of ordered arguments,
- and returning full delta feature set if no ordered arguments are given.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#[]
-\family default
- – constructor that takes either an arbitrary number of ordered arguments,
- or a field of named arguments (
-\family typewriter
-:marking
-\family default
-, 
-\family typewriter
-:firing
-\family default
-, 
-\family typewriter
-:gradient
-\family default
-, 
-\family typewriter
-:flux
-\family default
-, 
-\family typewriter
-:delta
-\family default
-, 
-\family typewriter
-:assignment
-\family default
-), identifying a (possibly) mixed set of features.
-\end_layout
-
-\begin_layout Standard
-Furthermore, class method 
-\family typewriter
-#new
-\family default
- is tweaked to make the returned instances own a PS of 
-\family typewriter
-Record
-\family default
- and a PS of 
-\family typewriter
-DataSet
-\family default
- 
-\emph on
-doubly parametrized
-\emph default
- by the instance.
- Therefore, also instance methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Record
-\family default
- – a PS of 
-\family typewriter
-Features.Record
-\family default
- PS parametrized by the 
-\family typewriter
-Features
-\family default
- instance.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#DataSet
-\family default
- – a PS of 
-\family typewriter
-Features.DataSet
-\family default
- PS parametrized by the 
-\family typewriter
-Features
-\family default
- instance.
-\end_layout
-
-\begin_layout Standard
-Other instance methods are:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#load
-\family default
- – delegated to the 
-\family typewriter
-Record
-\family default
- PS owned by the instance.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#extract_from
-\family default
- – extracts a feature set from the target object, returning a record.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Record
-\family default
- alias 
-\family typewriter
-#load
-\family default
- – constructs an instance from an array of values.
- The values must corresponds to the receiver feature set.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#+
-\family default
-, 
-\family typewriter
-#-
-\family default
-, 
-\family typewriter
-#*
-\family default
- – addition, subtraction, 
-\family typewriter
-Array
-\family default
--like multiplication for feature sets.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#labels
-\family default
- – array of feature labels.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reduce_features
-\family default
- – expects an argument identifying a set of features that is a subset of
- the receiver feature set, and returns that feature subset.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Marking
-\family default
-, 
-\family typewriter
-#Firing
-\family default
-, 
-\family typewriter
-#Flux
-\family default
-, 
-\family typewriter
-#Assignment
-\family default
- – selectors of a subset of the receiver feature set, accepting single array
- argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking
-\family default
-, 
-\family typewriter
-#firing
-\family default
-, 
-\family typewriter
-#flux
-\family default
-, 
-\family typewriter
-#assignment
-\family default
- – versions of the above selectors, that accept any number of arguments,
- and return full corresponding subsets if no arguments given.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Gradient
-\family default
-, 
-\family typewriter
-#Delta
-\family default
-, 
-\family typewriter
-#gradient
-\family default
-, 
-\family typewriter
-#delta
-\family default
- – selectors analogical to the above mentioned, but also accepting an optional
- named argument 
-\family typewriter
-:transitions
-\family default
- qualifying the features to select.
-\end_layout
-
-\begin_layout Standard
-Furthermore, 
-\family typewriter
-:Record
-\family default
- message is overloaded in such way, that when sent with an argument, it
- acts as an alias of 
-\family typewriter
-#load
-\family default
- record constructor.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Record
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-A record is basically an array, that remembers the features to which its
- values correspond.
- 
-\family typewriter
-Net::State::Features::Record
-\family default
- class is typically used as doubly parametrized PS, dependent firstly on
- a 
-\family typewriter
-Features
-\family default
- PS, and then on its particular instance.
- The owning feature set is accessible via 
-\family typewriter
-#features
-\family default
- class and instance method.
- Other class methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#load
-\family default
- – constructs a record from a given collection of values.
-\end_layout
-
-\begin_layout Standard
-Other instance methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#dump
-\family default
- – converts the record to a plain array, with optional :precision named
- argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#print
-\family default
- – pretty prints the record with feature names.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#fetch
-\family default
- – returns a feature.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#state
-\family default
- – constructs a state, using the receiver record, and a set of complementary
- marking clamps supplied in the argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reconstruct
-\family default
- – reconstructs a simulation from the receiver record.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Marking
-\family default
-, 
-\family typewriter
-#Firing
-\family default
-, 
-\family typewriter
-#Flux
-\family default
-, 
-\family typewriter
-#Assignment
-\family default
- – selects the values of the specified feature subsets from the receiver
- record.
- Expects a single array-type argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking
-\family default
-, 
-\family typewriter
-#firing
-\family default
-, 
-\family typewriter
-#flux
-\family default
-, 
-\family typewriter
-#assignment
-\family default
- – the versions of the above methods accepting any number of feature-identifying
- arguments.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Gradient
-\family default
-, 
-\family typewriter
-#Delta
-\family default
-, 
-\family typewriter
-#gradient
-\family default
-, 
-\family typewriter
-#delta
-\family default
- – selectors analogical to the above mentioned, but also accepting an optional
- named argument 
-\family typewriter
-:transitions
-\family default
- qualifying the features to select.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#euclidean_distance
-\family default
- – takes another record of the same feature set as an argument and computes
- the Euclidean distance to it.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-DataSet
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Net::DataSet
-\family default
- represents a sequence of records sampled from the underlying net using
- certain feature set.
- It is a subclass of 
-\family typewriter
-Hash
-\family default
-, whose keys represent sampling events, and whose values are plain arrays,
- from which corresponding 
-\family typewriter
-Record
-\family default
- instances can be fully reconstructed (via 
-\family typewriter
-Record.load
-\family default
- method).
- It is typically used as doubly parametrized PS, dependent firstly on a
- 
-\family typewriter
-Features
-\family default
- PS, and then on its particular instance.
- The owning feature set is accessible via 
-\family typewriter
-#features
-\family default
- class and instance method.
- Other class methods include:
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#events
-\family default
- – alias for 
-\family typewriter
-Hash#keys
-\family default
- – dataset keys represent sampling events.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reduce_features
-\family default
- – selects certain columns (features) of a dataset.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#timed?
-\family default
- – inquirer whether the dataset is timed
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#record
-\family default
- – reconstructs the 
-\family typewriter
-Record
-\family default
- instance corresponding to the given event.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#floor
-\family default
- – the nearest event smaller or equal to the argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#ceiling
-\family default
- – the nearest event greater or equal than the argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#records
-\family default
- – returns an array of 
-\family typewriter
-Record
-\family default
- instances revived from the receiver's values.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reconstruct
-\family default
- – recreates the simulation at the given event.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#interpolate
-\family default
- – interpolates the recording at the given point (event).
- Return value is the Record class instance.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#resample
-\family default
- – resamples the recording.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#distance
-\family default
- – computes the distance to another dataset.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#series
-\family default
- – returns the data series for the specified features.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#reduce_features
-\family default
- – reduces the dataset into another dataset with a different set of features.
- Reduction to a subset of features is always possible.
- Reduction to a set of features that is not a subset of the receiver's set
- of features is only possible if the former can be inferred from the latter.
- Generally, this is the case if net state can be reconstructed from a receiver's
- record.
- From this net state, the desired new feature set is then extracted.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Marking
-\family default
-, 
-\family typewriter
-#Firing
-\family default
-, 
-\family typewriter
-#Flux
-\family default
-, 
-\family typewriter
-#Assignment
-\family default
- – selects the values of the specified feature subsets from the receiver
- record.
- Expects a single array-type argument.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#marking
-\family default
-, 
-\family typewriter
-#firing
-\family default
-, 
-\family typewriter
-#flux
-\family default
-, 
-\family typewriter
-#assignment
-\family default
- – the versions of the above methods accepting any number of feature-identifying
- arguments.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#Gradient
-\family default
-, 
-\family typewriter
-#Delta
-\family default
-, 
-\family typewriter
-#gradient
-\family default
-, 
-\family typewriter
-#delta
-\family default
- – selectors analogical to the above mentioned, but also accepting an optional
- named argument 
-\family typewriter
-:transitions
-\family default
- qualifying the features to select.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#to_csv
-\family default
- – outputs the dataset in the CSV format.
-\end_layout
-
-\begin_layout Itemize
-
-\family typewriter
-#plot
-\family default
- – plots the dataset.
-\end_layout
-
-\begin_layout Part*
-
-\family typewriter
-Agent
-\family default
- class
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-YPetri::Agent
-\family default
- / 
-\family typewriter
-YNelson::Agent
-\family default
- are dumb agents that represent and assist the user.
- Originally, this class was named 
-\family typewriter
-Manipulator
-\family default
-, but 
-\family typewriter
-Agent
-\family default
- is shorter.
- 
-\family typewriter
-Agent
-\family default
- does provide textual user interface, but it does not completely encapsulate
- 
-\family typewriter
-YPetri
-\family default
- (
-\family typewriter
-YNelson
-\family default
-) interface.
- Rather, it defines a number of top-level DSL commands (methods) available
- upon calling '
-\family typewriter
-include YPetri
-\family default
-' / '
-\family typewriter
-include YNelson
-\family default
-'.
- 
-\family typewriter
-Agent
-\family default
- is not a part of the core object model of 
-\family typewriter
-YPetri
-\family default
- / 
-\family typewriter
-YNelson
-\family default
-, and it is hotter than other parts of 
-\family typewriter
-YPetri
-\family default
- / 
-\family typewriter
-YNelson
-\family default
-.
- For basic use, see the tutorial (
-\begin_inset Quotes eld
-\end_inset
-
-Introduction to 
-\family typewriter
-YNelson
-\family default
-
-\begin_inset Quotes erd
-\end_inset
-
-).
- For detailed description of 
-\family typewriter
-Agent
-\family default
-'s assets, see the class documentation.
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-\begin_inset CommandInset bibtex
-LatexCommand bibtex
-bibfiles "/home/boris/b/8oav/hos/hos"
-options "plainnat"
-
-\end_inset
-
-
-\end_layout
-
-\end_body
-\end_document