Chapter 4. Sequence Formats and Inheritance

This chapter applies concepts and techniques from previous chapters to a concrete project: handling sequence files. The chapter also introduces a few new techniques including a very important one called class inheritance. The code developed in this chapter will also be incorporated into later chapters.

Class inheritance allows you to define a new class by inheriting from other classes ”altering or making additions as needed. It's a style of software reuse that is particular to object-oriented design.

The first class developed in this chapter is a simple one: reading and writing files. Using inheritance, you can extend that class to a new one that can recognize, read, and write data in several different biological sequence datafile formats.

The goal is, as always, to learn enough about Perl to develop software for your own needs. The code in this chapter is designed with this goal in mind. In particular, the exercises at the end of the chapter will ask you to extend and improve the code in various ways.