Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

3.1 What Is Object-Oriented Programming?

Object-oriented programming is
a way to organize code so it interacts in certain prescribed ways,
obeying certain rules about how the data and subroutines are
organized. In other words, it imposes a certain programming
discipline that can lead to better and more reliable code.

The key idea of OO programming is that all data is stored and
modified with special data structures called
objects, and each kind of object can be accessed
only by its defined subroutines called methods.
The user of an OO class is typically spared the effort of directly
manipulating data, and can use class methods for this instead.

The promise of this OO structure of program code is that it makes the
resulting programs cleanly designed, more reliable, easier to reuse
in other programs, and easier to modify and improve. In essence, the
approach imposes certain restrictions on what a programmer can do
with the data and subroutines at hand.

Proponents of the OO approach cite the benefits this extra discipline
provides. It is certainly true that you can follow good programming
practices without using an OO approach. However, OO does provide a
well-defined framework for encouraging discipline and good
programming practices. In a very flexible language such as Perl, good
practices can sometimes be easier to enforce in the framework of OO.
We'll see how this comes about in the examples that
follow.

3.1.1 Why Object-Oriented Programming?

It is often important and necessary to weigh the costs and benefits
of a given system against the alternatives in an applied engineering
discipline such as programming. The decision to use OO programming,
declarative programming, or some other paradigm, is often subject to
religious debates, with some enthusiasts promoting their favorite
approach against all comers. This is especially relevant to the Perl
programmer, because Perl allows you to write in the declarative or in
the OO style. You should know that OO programming
isn't always the correct choice for a programming
project. Despite the real benefits it can confer upon a software
development project, it can also have certain costs; these costs and
benefits should be weighed against each other.

For instance, some types of software lend themselves more readily to
abstracting with OO techniques than others. Object-oriented software
development can sometimes take longer due to the overhead associated
with its level of abstraction. OO software sometimes runs slower than
other approaches; this has certainly been true in Perl, and although
not usually a deal breaker, it is sometimes an important
consideration. (Current work on the upcoming Perl 6 is addressing
this performance issue.)

In spite of these strictures, OO programming is often an excellent
choice; it has become a key approach to writing software in the Perl
language.

3.1.2 Terminology

Object

An object is a collection of data that logically belongs together.

For instance, you might have a genome object that would have such
attributes
(or parts) as the name of the organism, the DNA sequence data, the
start and end points for each exon, the genes with their associated
lists of exons, and so forth. The exact nature of an object is a
matter of logic and convenience, and in the end, it depends on the
judgment of the programmer as to what collection of attributes makes
an object that will accomplish the goals at hand.

A standard term in computer science for a collection of data is a
data structure. Data structures are often studied
in terms of accomplishing certain
algorithms. It is often the case that the
fastest, cleverest way to compute something relies upon putting the
data into a special data structure that makes a fast algorithm
possible.[1]

[1] This point really highlights the importance
of spending some time on design at the beginning of your programming,
and the importance of using a good efficiency tester such as
Benchmark.pm to evaluate alternate
solutions.

In Perl, objects are usually implemented as references to hashes and
are marked with their class name. The Perl function
bless marks a reference with a class name, as will
be explained in this chapter. The Perl function
ref can be used to see what class name an object
is marked with.

Method

In OO programming, a subroutine called a method is associated with an
object. Each type of object has one or more methods that it can call.
In this style of programming, the only way to access the data in an
object is by the defined methods of the class. This restriction is
meant to increase reliability, reusability, and maintainability.

In Perl, methods are implemented as Perl subroutines, although they
behave slightly differently from other subroutines. Methods are
called from an object, and they know what object
they're called on; they don't need
to be explicitly imported, and they exist in a hierarchy of classes.
If you know how to use Perl subroutines, methods are an easy next
step.

Class

Together, the object definitions and the collection of methods for
them defines a class. A specific
object (say, a genome object for C.
elegans) is called an instance of a
class.

Classes can be related to each other so methods can be inherited into
a class from another class. In Perl, classes are implemented as
namespaces, by means of the package directive.

Now that you're familiar with the language of OO
programming, let's see how it's
used.