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| Foreword | |
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| Preface | |
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| Object-Oriented Programming in Perl | |
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| Modular Programming with Perl | |
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| What Is a Module? | |
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| Why Perl Modules? | |
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| Namespaces | |
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| Packages | |
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| Defining Modules | |
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| Storing Modules | |
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| Writing Your First Perl Module | |
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| Using Modules | |
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| CPAN Modules | |
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| Exercises | |
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| Data Structures and String Algorithms | |
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| Basic Perl Data Types | |
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| References | |
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| Matrices | |
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| Complex Data Structures | |
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| Printing Complex Data Structures | |
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| Data Structures in Action | |
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| Dynamic Programming | |
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| Approximate String Matching | |
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| Resources | |
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| Exercises | |
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| Object-Oriented Programming in Perl | |
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| What Is Object-Oriented Programming? | |
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| Using Perl Classes (Without Writing Them) | |
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| Objects, Methods, and Classes in Perl | |
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| Arrow Notation (-[right angle bracket]) | |
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| Gene1: An Example of a Perl Class | |
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| Details of the Gene1 Class | |
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| Gene2.pm: A Second Example of a Perl Class | |
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| Gene3.pm: A Third Example of a Perl Class | |
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| How AUTOLOAD Works | |
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| Cleaning Up Unused Objects with DESTROY | |
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| Gene.pm: A Fourth Example of a Perl Class | |
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| How to Document a Perl Class with POD | |
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| Additional Topics | |
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| Resources | |
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| Exercises | |
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| Sequence Formats and Inheritance | |
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| Inheritance | |
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| FileIO.pm: A Class to Read and Write Files | |
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| SeqFileIO.pm: Sequence File Formats | |
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| Resources | |
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| Exercises | |
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| A Class for Restriction Enzymes | |
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| Envisioning an Object | |
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| Rebase.pm: A Class Module | |
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| Restriction.pm: Finding Recognition Sites | |
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| Drawing Restriction Maps | |
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| Resources | |
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| Exercises | |
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| Perl and Bioinformatics | |
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| Perl and Relational Databases | |
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| One Perl, Many Databases | |
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| Popular Relational Databases | |
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| Relational Database Definitions | |
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| Structured Query Language | |
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| Administering Your Database | |
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| Relational Database Design | |
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| Perl DBI and DBD Interface Modules | |
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| A Rebase Database Implementation | |
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| Additional Topics | |
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| Resources | |
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| Exercises | |
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| Perl and the Web | |
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| How the Web Works | |
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| Web Servers and Browsers | |
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| The Common Gateway Interface | |
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| Rebase: Building Dynamic Web Pages | |
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| Exercises | |
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| Perl and Graphics | |
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| Computer Graphics | |
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| GD | |
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| Adding GD Graphics to Restrictionmap.pm | |
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| Making Graphs | |
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| Resources | |
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| Exercises | |
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| Introduction to Bioperl | |
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| The Growth of Bioperl | |
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| Installing Bioperl | |
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| Testing Bioperl | |
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| Bioperl Problems | |
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| Overview of Objects | |
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| bptutorial.pl | |
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| bptutorial.pl: sequence_manipulation Demo | |
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| Using Bioperl Modules | |
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| Appendixes | |
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| Perl Summary | |
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| Installing Perl | |
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| Index | |