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Contents Listing

Foreword



Preface





Part I. Object-Oriented Programming in Perl



1. Modular Programming with Perl

What Is a Module?

Why Perl Modules?

Namespaces

Packages

Defining Modules

Storing Modules

Writing Your First Perl Module

Using Modules

CPAN Modules

Exercises



2. Data Structures and String Algorithms

Basic Perl Data Types

References

Matrices

Complex Data Structures

Printing Complex Data Structures

Data Structures in Action

Dynamic Programming

Approximate String Matching

Resources

Exercises



3. Object-Oriented Programming in Perl

What Is Object-Oriented Programming?

Using Perl Classes (Without Writing Them)

Objects, Methods, and Classes in Perl

Arrow Notation (->)

Gene1: An Example of a Perl Class

Details of the Gene1 Class

Gene2.pm: A Second Example of a Perl Class

Gene3.pm: A Third Example of a Perl Class

How AUTOLOAD Works

Cleaning Up Unused Objects with DESTROY

Gene.pm: A Fourth Example of a Perl Class

How to Document a Perl Class with POD

Additional Topics

Resources

Exercises



4. Sequence Formats and Inheritance

Inheritance

FileIO.pm: A Class to Read and Write Files

SeqFileIO.pm: Sequence File Formats

Resources

Exercises



5. A Class for Restriction Enzymes

Envisioning an Object

Rebase.pm: A Class Module

Restriction.pm: Finding Recognition Sites

Drawing Restriction Maps

Resources

Exercises





Part II. Perl and Bioinformatics



6. Perl and Relational Databases

One Perl, Many Databases

Popular Relational Databases

Relational Database Definitions

Structured Query Language

Administering Your Database

Relational Database Design

Perl DBI and DBD Interface Modules

A Rebase Database Implementation

Additional Topics

Resources

Exercises



7. Perl and the Web

How the Web Works

Web Servers and Browsers

The Common Gateway Interface

Rebase: Building Dynamic Web Pages

Exercises



8. Perl and Graphics

Computer Graphics

GD

Adding GD Graphics to Restrictionmap.pm

Making Graphs

Resources

Exercises



9. Introduction to Bioperl

The Growth of Bioperl

Installing Bioperl

Testing Bioperl

Bioperl Problems

Overview of Objects

bptutorial.pl

bptutorial.pl: sequence_manipulation Demo

Using Bioperl Modules





Part III. Appendixes



A. Perl Summary



B. Installing Perl



Index