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List of contents
Foreword;
Preface;
About This Book;
What You Need to Know to Use This Book;
Organization of This Book;
Conventions Used in This Book;
Comments and Questions;
Acknowledgments;
Object-Oriented Programming in Perl;
Chapter 1: Modular Programming with Perl;
1.1 What Is a Module?;
1.2 Why Perl Modules?;
1.3 Namespaces;
1.4 Packages;
1.5 Defining Modules;
1.6 Storing Modules;
1.7 Writing Your First Perl Module;
1.8 Using Modules;
1.9 CPAN Modules;
1.10 Exercises;
Chapter 2: Data Structures and String Algorithms;
2.1 Basic Perl Data Types;
2.2 References;
2.3 Matrices;
2.4 Complex Data Structures;
2.5 Printing Complex Data Structures;
2.6 Data Structures in Action;
2.7 Dynamic Programming;
2.8 Approximate String Matching;
2.9 Resources;
2.10 Exercises;
Chapter 3: Object-Oriented Programming in Perl;
3.1 What Is Object-Oriented Programming?;
3.2 Using Perl Classes (Without Writing Them);
3.3 Objects, Methods, and Classes in Perl;
3.4 Arrow Notation (->);
3.5 Gene1: An Example of a Perl Class;
3.6 Details of the Gene1 Class;
3.7 Gene2.pm: A Second Example of a Perl Class;
3.8 Gene3.pm: A Third Example of a Perl Class;
3.9 How AUTOLOAD Works;
3.10 Cleaning Up Unused Objects with DESTROY;
3.11 Gene.pm: A Fourth Example of a Perl Class;
3.12 How to Document a Perl Class with POD;
3.13 Additional Topics;
3.14 Resources;
3.15 Exercises;
Chapter 4: Sequence Formats and Inheritance;
4.1 Inheritance;
4.2 FileIO.pm: A Class to Read and Write Files;
4.3 SeqFileIO.pm: Sequence File Formats;
4.4 Resources;
4.5 Exercises;
Chapter 5: A Class for Restriction Enzymes;
5.1 Envisioning an Object;
5.2 Rebase.pm: A Class Module;
5.3 Restriction.pm: Finding Recognition Sites;
5.4 Drawing Restriction Maps;
5.5 Resources;
5.6 Exercises;
Perl and Bioinformatics;
Chapter 6: Perl and Relational Databases;
6.1 One Perl, Many Databases;
6.2 Popular Relational Databases;
6.3 Relational Database Definitions;
6.4 Structured Query Language;
6.5 Administering Your Database;
6.6 Relational Database Design;
6.7 Perl DBI and DBD Interface Modules;
6.8 A Rebase Database Implementation;
6.9 Additional Topics;
6.10 Resources;
6.11 Exercises;
Chapter 7: Perl and the Web;
7.1 How the Web Works;
7.2 Web Servers and Browsers;
7.3 The Common Gateway Interface;
7.4 Rebase: Building Dynamic Web Pages;
7.5 Exercises;
Chapter 8: Perl and Graphics;
8.1 Computer Graphics;
8.2 GD;
8.3 Adding GD Graphics to Restrictionmap.pm;
8.4 Making Graphs;
8.5 Resources;
8.6 Exercises;
Chapter 9: Introduction to Bioperl;
9.1 The Growth of Bioperl;
9.2 Installing Bioperl;
9.3 Testing Bioperl;
9.4 Bioperl Problems;
9.5 Overview of Objects;
9.6 bptutorial.pl;
9.7 bptutorial.pl: sequence_manipulation Demo;
9.8 Using Bioperl Modules;
Appendixes;
Perl Summary;
Command Interpretation;
Comments;
Scalar Values and Scalar Variables;
Assignment;
Statements and Blocks;
Arrays;
Hashes;
Complex Data Structures;
Operators;
Operator Precedence;
Basic Operators;
Conditionals and Logical Operators;
Binding Operators;
Loops;
Input/Output;
Regular Expressions;
Scalar and List Context;
Subroutines;
Modules and Packages;
Object-Oriented Programming;
Built-in Functions;
Installing Perl;
Installing Perl on Your Computer;
Versions of Perl;
Internet Access;
Downloading;
How to Run Perl Programs;
Finding Help;
Colophon;
