Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

Chapter 3. Object-Oriented Programming in Perl

In Chapter 1, you saw how modules are defined and used, and in
Chapter 2, how references and data structures work. Now,
it's time to introduce the important concepts and
techniques of object-oriented programming in Perl that are based on
modules and references.

Object-oriented (OO) programming is one of the
most important approaches to writing programs, and it is an approach
that has been well supported by Perl for quite a while. Other OO
languages of interest include Java, C++, and Smalltalk. Many Perl
modules are written in an OO style, and their proper use requires
some fundamental understanding of the OO approach. Luckily, the key
concepts are fairly simple.

Perl easily supports both declarative and OO programming. (Perl was
originally a declarative language only; the OO style was added fairly
early on.)
Declarative programming is
characterized by code that declares variables and subroutines,
conditional tests, if-else branches, and loops, and various
arithmetic, logical, and string operators. It is up to you to manage
the definition and use of the variables and subroutines so that they
interact in appropriate ways. (You'll see shortly
how object-oriented programming imposes additional constraints that
help you create well-behaved programs.) Many declarative programming
languages are well established, including Perl and such stalwarts as
C, FORTRAN, and BASIC, to name just a few. By this point, assuming
you have some experience programming in Perl, you should be fairly
comfortable with the declarative style.

The first part of this chapter is an overview of OO programming and
how OO Perl modules are used. If you're a beginning
Perl programmer, you'll find them easy to use
because they rarely require you to know how to write OO Perl code.
Depending on your needs and goals, this might be all the information
you'll require from this chapter.

As a more advanced programmer, you'll sometimes need
to write your own OO bioinformatics software. If
you're such a programmer, the second part of this
chapter will be of greatest interest to you. However, because the
material is developed incrementally, you will most likely want to
read the chapter in order from beginning to end.

Perl makes clever and simple use of existing mechanisms to support OO
programming. Perl packages and modules are used to define OO classes,
Perl references define OO objects, and Perl subroutines define OO
methods. The definitions of these terms will become clear as you read
the chapter, but in brief, OO software is organized into classes that
contain data called objects. Subroutines called methods operate on
the objects.

Over the course of this chapter, I'll develop a
small example object module, Gene.pm, to
demonstrate the essentials of OO Perl. Gene.pm is
developed in four stages so you can learn the OO style gradually. The
final code for Gene.pm serves as a template from
which you can begin developing your own OO software.