OOP and object parametrization - oop

I am supposed to develop a program, which will heavily depend on input data at runtime (data for initialization, read from XML) and I would like to ask for good OOP practice regarding object/architecture design.
Situation
I have the following objects, object_A, object_B, object_C, each of them has a specified objective.
object_A = evaluation of equations, requires input, produces output
object_B = evaluation of equations, requires input, produces output
object_C = requires data from object_A and object_B as input, produces output
Then there is object_D, which passes the data and calls functions among these objects_A/B/C.
There are 2 ways to tackle this situation that I know of :
a) Inheritance
object_D inherits from object_A, object_B, object_C. Data are passed by appointing appropriate structures in objects_A/_B/_C using "this->", virtual functions in objects_A/_B/_C can then call back to object_D.
hierarchical approach
objects are concealed
difficult to parametrize the object_A/_B/_C (parameters need to travel all the way up in the hierarchy to base classes)
b) Passing pointers
Create object_A/_B/_C, by passing parameters in constructor. Then pass pointers of these objects to constructor of object_D.
no information hiding, all objects are visible
hierarchy might be unclear, especially when there are more levels
easy to pass initialization parameters
Question
What is an appropriate way of handling software architecture, where many objects require passing initialization parameters at runtime?

I think your question is broad and can have more than one good answer. However, I think your scenario can be solved in one of two ways:
Eventing: Instead of tightly coupling your classes using inheritance, you can use events. For instance when Object A finishes processing it raise an event called 'ClassAFinished'. Then you have to create an event handler for ClassAFinish Event that will in turns pass objectA's output to other objects that rely on Object A output.
Second way is Chain of Responsibility design pattern. Since your question is related to OOP I think it's reasonable to use this design pattern. In a nutshell Chain of Responsibility is a design pattern that you use it when you have a series (chain) of objects, each of which will do specific processing (responsibility), but each one of them can't begin processing until it received data from the previous object. When it finishes processing it'll send its output to the next object and so forth.
These are 2 main ideas that I wanted to share with you.

Related

Code design: Who's responsible for changing object data?

Assuming I have some kind of data structure to work on (for example images) which I want to pre- and postprocess in different ways to make further processing steps easier. What's the best way to implement this responsibility with an OOP language like C++?
Further assuming I have a lot of different processing algorithms with inherent complexity I very likely want to encapsulate them in dedicated classes. This means though that the algorithm implementations externally have to set some kind of info in my data to indicate it having been processed. And that also doesn't look like clean design to me because having been processed seems like an info associated with the data and thus something the data object itself should determine and set on its own.
It also looks like a very common source of error in complex applications: Someone implements another processing algorithm, forgets to set the flags in the data appropriately, something in completely different parts of the application won't work as expected and someone will have lots of fun spotting the error.
Can someone outline a general structure of a good and fail-save way to implement sth like this?
To make sure I understand what you are asking, here are my assumptions based on my reading of the question:
The data is some kind of binary format (presumably an image but as you say it could be anything) that can be represented as an array of bytes
There are a number of processing steps (I'll refer to them as transformations) that can be applied to the data
Some transformations depend on other such that, for example, you would like to avoid applying a transformation if its pre-requisite has not been applied. You would like it to be robust, so that attempting to apply an illegal transformation will be detected and prevented.
And the question is how to do this in an object-oriented way that avoids future bugs as the complexity of the program increases.
One way is to have the image data object, which encapsulates both the binary data and a record of the transformations that have been applied to it, be responsible for executing the transformation through a Transformation object delegate; and the Transformation objects implement both the processing algorithm and the knowledge of whether it can be applied based on previous transformations.
So you might define the following (excuse my Java-like naming style; it's been a long time since I've done C++):
An enumerated type called TransformationType
An abstract class called Transformer, with the following methods:
A method called 'getType' which returns a TransformationType
A method called 'canTransform' that accepts a list of TransformationType and returns a boolean. The list indicates transformations that have already been applied to the data, and the boolean indicates whether it is OK to execute this transformation.
A method called 'transform' that accepts an array of bytes and returns an array of (presumably modified) bytes
A class called BinaryData, containing a byte array and a list of TransformationType. This class implements the method 'void transform(Transformer t)' to do the following:
Query the transformer's 'canTransform' method, passing the list of transformation types; either throw an exception or return if canTransform returns false
Replace he byte array with the results of invoking t.transform(data)
Add the transfomer's type to the list
I think this accomplishes what you want - the image transformation algorithms are defined polymorphically in classes, but the actual application of the transformations is still 'controlled' by the data object. Hence we do not have to trust external code to do the right thing wrt setting / checking flags, etc.

What is the best way to show the work flow of a single class with UML

What is the best UML diagram type to use when trying to show how a class' behavior flows from one method to another?
I am trying to diagram existing code and the behavior I am looking at primarily involves private method calls, with a few calls to static objects outside the class. I don't feel that a sequence diagram would give the best detail in this case since the class in question doesn't interact with any other classes except for the very few static calls mentioned earlier.
What would fit best in this situation?
According to the UML Superstructure (http://www.omg.org/spec/UML), in the UML two kind of behaviors exist: emergent behaviors and executing behaviors.
An executing behavior is performed by an object (its host) and is the description of the behavior of this object.
An executing behavior is directly caused by the invocation of a behavioral feature of that object or by its creation. In either case, it is a consequence of the execution of an action by some related object. A behavior has access to the structural features of its host object. Objects that may host behaviors are specified by the concrete subtypes of the BehavioredClassifier metaclass.
Emergent behavior results from the interaction of one or more participant objects. If the participating objects are parts of a larger composite object, an emerging behavior can be seen as indirectly describing the behavior of the container object also. Nevertheless, an emergent behavior can result from the executing behaviors of the participant objects.
You can model behaviors by means of Activities or Interactions (actually you may also use state machines and use cases). Activities are more adapt to model executing behaviors while Interactions to model emergent behaviors.
Now if your class has many parts and its behavior you want to model consists in a "complex" interaction of its parts then probably an interaction diagram (sequence) may be the right choice. Otherwise, if the behavior you need to model, consists of a sequence of atomic actions an activity may be better. Consider in UML there is a specific actions to represent the invokation of a method (CallOperationAction) which takes as input pin the object reference you can retrieve by means of a dedicated action (ReadSelfAction). There is also an action to read an object attribute (ReadStructuralFeatureAction).
Also check the Foundational for Executable UML Models (FUML) http://www.omg.org/spec/FUML
While all of the previous answers are correct, I would like to add the option of using a State-Machine to define the behavior of the class. State machines allow you to show what is the current state of the class and how the state of the class changes as methods are called or events are received. Since you state that you are mostly modeling one class, I think the most important thing to show is what can be done (what method calls can be called) depending on the current state and how these method calls affect the state of the class. One think I really like about state machines is that they have relatively well defined semantics and also have ways to show information at different levels using composite and orthogonal states.
Broadly you have 2 choices (per #Silli's answer): sequence or activity diagram. I would probably have suggested sequence diag as first choice, however you say you don't think that's appropriate. Could you elaborate why?
Perhaps it's conditional logic? If so an activity diagram may be the better choice. It has more intuitive syntax for showing control flow than a sequence diagram. You could also show the static objects in separate swimlanes - so clearly differentiating calls to external objects. You can also illustrate parallel behaviour if that's relevant to you. Some good examples here if it helps.
hth.
I would recommend collaboration diagram (UML 1.x) renamed to Communication diagram (UML 2.x).
This may be better than sequence diagram, better because it may be more readable in your case.
A Communication diagram models the interactions between objects or parts in terms of sequenced messages. Communication diagrams represent a combination of information taken from Class, Sequence, and Use Case Diagrams describing both the static structure and dynamic behavior of a system.
http://en.wikipedia.org/wiki/Communication_diagram

Is it poor design to create objects that only execute code during the constructor?

In my design I am using objects that evaluate a data record. The constructor is called with the data record and type of evaluation as parameters and then the constructor calls all of the object's code necessary to evaluate the record. This includes using the type of evaluation to find additional parameter-like data in a text file.
There are in the neighborhood of 250 unique evaluation types that use the same or similar code and unique parameters coming from the text file.
Some of these evaluations use different code so I benefit a lot from this model because I can use inheritance and polymorphism.
Once the object is created there isn't any need to execute additional code on the object (at least for now) and it is used more like a struct; its kept on a list and 3 properties are used later.
I think this design is the easiest to understand, code, and read.
A logical alternative I guess would be using functions that return score structs, but you can't inherit from methods so it would make it kind of sloppy imo.
I am using vb.net and these classes will be used in an asp.net web app as well as in a distributed app.
thanks for your input
Executing code in a constructor is OK; but having only properties with no methods might be a violation of the tell don't ask principle: perhaps instead those properties should be private, and the code which uses ("asks") those properties should become methods of the class (which you can invoke or "tell").
In general, putting code that does anything significant in the constructor a not such a good idea, because you'll eventually get hamstrung on the rigid constructor execution order when you subclass.
Constructors are best used for getting your object to a consistent state. "Real" work is best handled in instance methods. With the work implemented as a method, you gain:
separation of what you want to evaluate from when you want to evaluate it.
polymorphism (if using virtual methods)
the option to split up the work into logical pieces, implementing each piece as a concrete template method. These template methods can be overridden in subclasses, which provides for "do it mostly like my superclass, but do this bit differently".
In short, I'd use methods to implement the main computation. If you're concerned that an object will be created without it's evaluation method being called, you can use a factory to create the objects, which calls the evaluate method after construction. You get the safety of constructors, with the execution order flexibility of methods.

Object-oriented programming & transactions

A little intro:
Class contains fields and methods (let me skip properties this time).
Fields represent a state of the class.
Methods describe behavior of the class.
In a well-designed class, a method won't change the class's state if it throws an exception, right? (In other words, whatever happens, class's state shouldn't be corrupted)
Question:
Is there a framework, a design pattern, best practice or a programming language to call a sequence of methods in a transactional style, so that either class's state don't get changed (in case of exception), or everything succeeds?
E.g.:
// the class foo is now in the state S1
foo.MoveToState2();
// it is now (supposed to be) in the state S2
foo.MoveToFinalState();
// it is now (supposed to be) in the state, namely, S3
Surely, an exception might occur both in MoveToState2() and MoveToFinalState(). But from this block of code I want the class foo to be either in the state S1 or S3.
This is a simple scenario with a single class involved, no if's, no while's, no side effects, but I hope the idea is clear.
Take a look at the Memento pattern
The memento pattern is a software design pattern that provides the ability to restore an object to its previous state (undo via rollback).
Not the most efficient method, but you could have an object that represents your transactional data. When you start a transaction, make a copy of the data and perform all operations on that. When the transaction ends successfully, move the copy to your real data - this can be done using pointers, so need not be too inefficient.
Functional programming is a paradigm that seems to fit well to transactional computations. Since no side-effects are allowed without explicit declaration, you have full control of all data flow.
Therefore software transactional memory can be expressed easily in functional terms - See STM for F#
The key idea is the concept of monads. A monad can be used to model an arbitrary computation through two primitives: Return to return a value and Bind to sequence two computations. Using these two, you can model a transactional monad that controls and saves all state in form of continuations.
One could try to model these in an object-oriented way through a State+Memento pattern, but generally, transactions in imperative languages (like the common OO-ones) are much more difficult to implement since you can perform arbitrary side-effects. But of course you can think of an object defining a transaction scope, that saves, validates and restores data as needed, given they expose a suitable interface for this (the patterns I mentioned above).
The simplest and most reliable "pattern" to use here is an immutable data structure.
Instead of writing:
foo.MoveToState2();
foo.MoveToFinalState();
You write:
MyFoo foo2 = foo.MoveToState2();
MyFoo finalFoo = foo2.MoveToFinalState();
And implement the methods accordingly - that is, MoveToState2 does not actually change anything about MyFoo, it creates a new MyFoo that is in state 2. Similarly with the final state.
This is how the string classes in most OO languages work. Many OO languages are also starting to implement (or have already implemented) immutable collections. Once you have the building blocks, it's fairly straightforward to create an entire immutable "entity".
This would be pretty ugly to implement everywhere, but just saving the state locally, then restoring it in the case of an exception would work in simple scenarios. You'd have to catch and rethrow the exception, which may lose some context in some languages. It might be better to wrap it if possible to retain the context.
try {
save state in local variables
move to new state
} catch (innerException) {
restore state from local variables
throw new exception( innerException )
}
When using object copy approach, you have to watch out that the statements to be rolled-back are only affecting the object's or data itself (and aggregates).
But things are getting really difficult if the side-effects of the statements are "more external". For example I/O operations, network calls. You always have to analyze the overall state-changes of your statements.
It gets also really tricky if you touch static data (or evil mutable singletons). Reverting this data isolated is difficult, because other threads could have modified them in between (you could face lost updates).
Reverting/rollback to the past is often not so trivial ;)
I would also consider the saga pattern, you could pass a copy of the objects current state into MoveToState2 and if it throws an exception you could catch that internally and use the copy of the original state to rollback. You would have to do the same with MoveToState3 too. If however the server crashed during a rollback you might still get corrupted state, that's why databases are so good.
Transactional memory fits here the best.
An option could be a transactional storage. Sample implementation you can find here:
http://www.codeproject.com/KB/dotnet/Transactional_Repository.aspx
Memento pattern
Also let me describe a possible pattern on how to implement such behavior:
Define a base class TransactionalEntity. This class contains dictionary of properties.
All your transactional classes inherit from the TransactionalEntity and should operate over some sort of Dependency Properties/Fields, i.e. properties(getters/setters) which store it's values not in local class fields, but in dictionary, which is stored in the base class.
Then you define TransactionContext class. TransactionContext class internally contains a set of dictionaries (one dictionary for each entity that participates in the transaction) and when a transactional entity participates in transaction, it writes all data to the dictionary in the transaction context. Then all you need is basically four methods:
TransactionContext.StartTransaction();
TransactionalEntity.JoinTransaction(TransactionContext context); //if your language/framework supports Thread Static fields, then you do not need this method
TransactionContext.CommitTransaction();
TransactionContext.RollbackTransaction();
To sum up, you need to store state in base class TransactionalEntity and during transaction TransactionalEntity will cooperate with TransactionContext.
I hope, I've explained it well enough.
I think a Command Pattern could be well suited to this problem.
Linky.
I was astonished that no one suggested explicitly the simplest pattern to use .. the State Pattern
In this way you can also eliminate that 'finalState' method and just use 'handle()'.
How do you know which final state is?
The memento pattern is best used with the Command pattern, and usually applies to GUI operations to implement the undo/redo feature.
Fields represent a state of the class
Fields represents the state of the instanced object. You use many times wrong definitions of the OOP terms. Review and correct.

Is a function an example of encapsulation?

By putting functionality into a function, does that alone constitute an example of encapsulation or do you need to use objects to have encapsulation?
I'm trying to understand the concept of encapsulation. What I thought was if I go from something like this:
n = n + 1
which is executed out in the wild as part of a big body of code and then I take that, and put it in a function such as this one, then I have encapsulated that addition logic in a method:
addOne(n)
n = n + 1
return n
Or is it more the case that it is only encapsulation if I am hiding the details of addOne from the outside world - like if it is an object method and I use an access modifier of private/protected?
I will be the first to disagree with what seems to be the answer trend. Yes, a function encapsulates some amount of implementation. You don't need an object (which I think you use to mean a class).
See Meyers too.
Perhaps you are confusing abstraction with encapsulation, which is understood in the broader context of object orientation.
Encapsulation properly includes all three of the following:
Abstraction
Implementation Hiding
Division of Responsibility
Abstraction is only one component of encapsulation. In your example you have abstracted the adding functionality from the main body of code in which it once resided. You do this by identifying some commonality in the code - recognizing a concept (addition) over a specific case (adding the number one to the variable n). Because of this ability, abstraction makes an encapsulated component - a method or an object - reusable.
Equally important to the notion of encapsulation is the idea of implementation hiding. This is why encapsulation is discussed in the arena of object orientation. Implementation hiding protects an object from its users and vice versa. In OO, you do this by presenting an interface of public methods to the users of your object, while the implementation of the object takes place inside private methods.
This serves two benefits. First, by limiting access to your object, you avoid a situation where users of the object can leave the object in an invalid state. Second, from the user's perspective, when they use your object they are only loosely coupled to it - if you change your implementation later on, they are not impacted.
Finally, division of responsility - in the broader context of an OO design - is something that must be considered to address encapsulation properly. It's no use encapsulating a random collection of functions - responsibility needs to be cleanly and logically defined so that there is as little overlap or ambiguity as possible. For example, if we have a Toilet object we will want to wall off its domain of responsibilities from our Kitchen object.
In a limited sense, though, you are correct that a function, let's say, 'modularizes' some functionality by abstracting it. But, as I've said, 'encapsulation' as a term is understood in the broader context of object orientation to apply to a form of modularization that meets the three criteria listed above.
Sure it is.
For example, a method that operates only on its parameters would be considered "better encapsulated" than a method that operates on global static data.
Encapsulation has been around long before OOP :)
A method is no more an example of encapsulation than a car is an example of good driving. Encapsulation isn't about the synax, it is a logical design issue. Both objects and methods can exhibit good and bad encapsulation.
The simplest way to think about it is whether the code hides/abstracts the details from other parts of the code that don't have a need to know/care about the implementation.
Going back to the car example:
Automatic transmission offers good encapsulation: As a driver you care about forward/back and speed.
Manual Transmission is bad encapsulation: From the driver's perspective the specific gear required for low/high speeds is generally irrelevant to the intent of the driver.
No, objects aren't required for encapsulation. In the very broadest sense, "encapsulation" just means "hiding the details from view" and in that regard a method is encapsulating its implementation details.
That doesn't really mean you can go out and say your code is well-designed just because you divided it up into methods, though. A program consisting of 500 public methods isn't much better than that same program implemented in one 1000-line method.
In building a program, regardless of whether you're using object oriented techniques or not, you need to think about encapsulation at many different places: hiding the implementation details of a method, hiding data from code that doesn't need to know about it, simplifying interfaces to modules, etc.
Update: To answer your updated question, both "putting code in a method" and "using an access modifier" are different ways of encapsulating logic, but each one acts at a different level.
Putting code in a method hides the individual lines of code that make up that method so that callers don't need to care about what those lines are; they only worry about the signature of the method.
Flagging a method on a class as (say) "private" hides that method so that a consumer of the class doesn't need to worry about it; they only worry about the public methods (or properties) of your class.
The abstract concept of encapsulation means that you hide implementation details. Object-orientation is but one example of the use of ecnapsulation. Another example is the language called module-2 that uses (or used) implementation modules and definition modules. The definition modules hid the actual implementation and therefore provided encapsulation.
Encapsulation is used when you can consider something a black box. Objects are a black box. You know the methods they provide, but not how they are implemented.
[EDIT]
As for the example in the updated question: it depends on how narrow or broad you define encapsulation. Your AddOne example does not hide anything I believe. It would be information hiding/encapsulation if your variable would be an array index and you would call your method moveNext and maybe have another function setValue and getValue. This would allow people (together maybe with some other functions) to navigate your structure and setting and getting variables with them being aware of you using an array. If you programming language would support other or richer concepts you could change the implementation of moveNext, setValue and getValue with changing the meaning and the interface. To me that is encapsulation.
It's a component-level thing
Check this out:
In computer science, Encapsulation is the hiding of the internal mechanisms and data structures of a software component behind a defined interface, in such a way that users of the component (other pieces of software) only need to know what the component does, and cannot make themselves dependent on the details of how it does it. The purpose is to achieve potential for change: the internal mechanisms of the component can be improved without impact on other components, or the component can be replaced with a different one that supports the same public interface.
(I don't quite understand your question, let me know if that link doesn't cover your doubts)
Let's simplify this somewhat with an analogy: you turn the key of your car and it starts up. You know that there's more to it than just the key, but you don't have to know what is going on in there. To you, key turn = motor start. The interface of the key (that is, e.g., the function call) hides the implementation of the starter motor spinning the engine, etc... (the implementation). That's encapsulation. You're spared from having to know what's going on under the hood, and you're happy for it.
If you created an artificial hand, say, to turn the key for you, that's not encapsulation. You're turning the key with additional middleman cruft without hiding anything. That's what your example reminds me of - it's not encapsulating implementation details, even though both are accomplished through function calls. In this example, anyone picking up your code will not thank you for it. They will, in fact, be more likely to club you with your artificial hand.
Any method you can think of to hide information (classes, functions, dynamic libraries, macros) can be used for encapsulation.
Encapsulation is a process in which attributes(data member) and behavior(member function) of a objects in combined together as a single entity refer as class.
The Reference Model of Open Distributed Processing - written by the International Organisation for Standardization - defines the following concepts:
Entity: Any concrete or abstract thing of interest.
Object: A model of an entity. An object is characterised by its behaviour and, dually, by its state.
Behaviour (of an object): A collection of actions with a set of constraints on when they may occur.
Interface: An abstraction of the behaviour of an object that consists of a subset of the interactions of that object together with a set of constraints on when they may occur.
Encapsulation: the property that the information contained in an object is accessible only through interactions at the interfaces supported by the object.
These, you will appreciate, are quite broad. Let us see, however, whether putting functionality within a function can logically be considered to constitute towards encapsulation in these terms.
Firstly, a function is clearly a model of a, 'Thing of interest,' in that it represents an algorithm you (presumably) desire executed and that algorithm pertains to some problem you are trying to solve (and thus is a model of it).
Does a function have behaviour? It certainly does: it contains a collection of actions (which could be any number of executable statements) that are executed under the constraint that the function must be called from somewhere before it can execute. A function may not spontaneously be called at any time, without causal factor. Sounds like legalese? You betcha. But let's plough on, nonetheless.
Does a function have an interface? It certainly does: it has a name and a collection of formal parameters, which in turn map to the executable statements contained in the function in that, once a function is called, the name and parameter list are understood to uniquely identify the collection of executable statements to be run without the calling party's specifying those actual statements.
Does a function have the property that the information contained in the function is accessible only through interactions at the interfaces supported by the object? Hmm, well, it can.
As some information is accessible via its interface, some information must be hidden and inaccessible within the function. (The property such information exhibits is called information hiding, which Parnas defined by arguing that modules should be designed to hide both difficult decisions and decisions that are likely to change.) So what information is hidden within a function?
To see this, we should first consider scale. It's easy to claim that, for example, Java classes can be encapsulated within a package: some of the classes will be public (and hence be the package's interface) and some will be package-private (and hence information-hidden within the package). In encapsulation theory, the classes form nodes and the packages form encapsulated regions, with the entirety forming an encapsulated graph; the graph of classes and packages is called the third graph.
It's also easy to claim that functions (or methods) themselves are encapsulated within classes. Again, some functions will be public (and hence be part of the class's interface) and some will be private (and hence information-hidden within the class). The graph of functions and classes is called the second graph.
Now we come to functions. If functions are to be a means of encapsulation themselves they they should contain some information public to other functions and some information that's information-hidden within the function. What could this information be?
One candidate is given to us by McCabe. In his landmark paper on cyclomatic complexity, Thomas McCabe describes source code where, 'Each node in the graph corresponds to a block of code in the program where the flow is sequential and the arcs correspond to branches taken in the program.'
Let us take the McCabian block of sequential execution as the unit of information that may be encapsulated within a function. As the first block within the function is always the first and only guaranteed block to be executed, we can consider the first block to be public, in that it may be called by other functions. All the other blocks within the function, however, cannot be called by other functions (except in languages that allow jumping into functions mid-flow) and so these blocks may be considered information-hidden within the function.
Taking these (perhaps slightly tenuous) definitions, then we may say yes: putting functionality within a function does constitute to encapsulation. The encapsulation of blocks within functions is the first graph.
There is a caveate, however. Would you consider a package whose every class was public to be encapsulated? According to the definitions above, it does pass the test, as you can say that the interface to the package (i.e., all the public classes) do indeed offer a subset of the package's behaviour to other packages. But the subset in this case is the entire package's behaviour, as no classes are information-hidden. So despite regorously satisfying the above definitions, we feel that it does not satisfy the spirit of the definitions, as surely something must be information-hidden for true encapsulation to be claimed.
The same is true for the exampe you give. We can certainly consider n = n + 1 to be a single McCabian block, as it (and the return statement) are a single, sequential flow of executions. But the function into which you put this thus contains only one block, and that block is the only public block of the function, and therefore there are no information-hidden blocks within your proposed function. So it may satisfy the definition of encapsulation, but I would say that it does not satisfy the spirit.
All this, of course, is academic unless you can prove a benefit such encapsulation.
There are two forces that motivate encapsulation: the semantic and the logical.
Semantic encapsulation merely means encapsulation based on the meaning of the nodes (to use the general term) encapsulated. So if I tell you that I have two packages, one called, 'animal,' and one called 'mineral,' and then give you three classes Dog, Cat and Goat and ask into which packages these classes should be encapsulated, then, given no other information, you would be perfectly right to claim that the semantics of the system would suggest that the three classes be encapsulated within the, 'animal,' package, rather than the, 'mineral.'
The other motivation for encapsulation, however, is logic.
The configuration of a system is the precise and exhaustive identification of each node of the system and the encapsulated region in which it resides; a particular configuration of a Java system is - at the third graph - to identify all the classes of the system and specify the package in which each class resides.
To logically encapsulate a system means to identify some mathematical property of the system that depends on its configuration and then to configure that system so that the property is mathematically minimised.
Encapsulation theory proposes that all encapsulated graphs express a maximum potential number of edges (MPE). In a Java system of classes and packages, for example, the MPE is the maximum potential number of source code dependencies that can exist between all the classes of that system. Two classes within the same package cannot be information-hidden from one another and so both may potentially form depdencies on one another. Two package-private classes in separate packages, however, may not form dependencies on one another.
Encapsulation theory tells us how many packages we should have for a given number of classes so that the MPE is minimised. This can be useful because the weak form of the Principle of Burden states that the maximum potential burden of transforming a collection of entities is a function of the maximum potential number of entities transformed - in other words, the more potential source code dependencies you have between your classes, the greater the potential cost of doing any particular update. Minimising the MPE thus minimises the maximum potential cost of updates.
Given n classes and a requirement of p public classes per package, encapsulation theory shows that the number of packages, r, we should have to minimise the MPE is given by the equation: r = sqrt(n/p).
This also applies to the number of functions you should have, given the total number, n, of McCabian blocks in your system. Functions always have just one public block, as we mentioned above, and so the equation for the number of functions, r, to have in your system simplifies to: r = sqrt(n).
Admittedly, few considered the total number of blocks in their system when practicing encapsulation, but it's readily done at the class/package level. And besides, minimising MPE is almost entirely entuitive: it's done by minimising the number of public classes and trying to uniformly distribute classes over packages (or at least avoid have most packages with, say, 30 classes, and one monster pacakge with 500 classes, in which case the internal MPE of the latter can easily overwhelm the MPE of all the others).
Encapsulation thus involves striking a balance between the semantic and the logical.
All great fun.
in strict object-oriented terminology, one might be tempted to say no, a "mere" function is not sufficiently powerful to be called encapsulation...but in the real world the obvious answer is "yes, a function encapsulates some code".
for the OO purists who bristle at this blasphemy, consider a static anonymous class with no state and a single method; if the AddOne() function is not encapsulation, then neither is this class!
and just to be pedantic, encapsulation is a form of abstraction, not vice-versa. ;-)
It's not normally very meaningful to speak of encapsulation without reference to properties rather than solely methods -- you can put access controls on methods, certainly, but it's difficult to see how that's going to be other than nonsensical without any data scoped to the encapsulated method. Probably you could make some argument validating it, but I suspect it would be tortuous.
So no, you're most likely not using encapsulation just because you put a method in a class rather than having it as a global function.