Mastering Perl for bioinformatics
Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capa...
| Autor principal: | |
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| Otros Autores: | |
| Formato: | Libro electrónico |
| Idioma: | Inglés |
| Publicado: |
Sebastopol, California ; Farnham :
O'Reilly
2003.
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| Edición: | First edition |
| Materias: | |
| Ver en Biblioteca Universitat Ramon Llull: | https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009627243006719 |
Tabla de Contenidos:
- Table 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; Part I; Modular Programming with Perl; What Is a Module?; Why Perl Modules?; Subroutines and Software Engineering; Modules and Libraries; Namespaces; Namespaces Compared with Scoping: my and use strict; Packages; Defining Modules; Storing Modules; Writing Your First Perl Module; An Example: Geneticcode.pm; Expanding Geneticcode.pm; Using Modules; Exporting Names; CPAN Modules; What's Available at CPAN?
- Searching CPANInstalling Modules Using CPAN.pm; Using the Newly Installed CPAN Module; Problems with CPAN Modules; Exercises; Data Structures and String Algorithms; Basic Perl Data Types; References; References to Scalars; Dereferencing; Anonymous data; References of References; References to Arrays; The arrow operator; Anonymous arrays; References to Hashes; Anonymous hashes; References to Subroutines; Anonymous subroutines; Passing references to subroutines; Returning references from subroutines; Symbolic Versus Hard References; Matrices; Two-Dimensional Matrices
- Higher-Dimensional MatricesSparse Arrays; Complex Data Structures; Hash with Array Values; Two-Dimensional Array of Hashes; Complex Data Structures; Printing Complex Data Structures; Data Structures in Action; The Problem of String Matching; Genetic Variability and String Matching; Dynamic Programming; Approximate String Matching; Edit Distance; A string matching program; Analysis; Resources; Exercises; Object-Oriented Programming in Perl; What Is Object-Oriented Programming?; Why Object-Oriented Programming?; Terminology; Using Perl Classes (Without Writing Them)
- Objects, Methods, and Classes in PerlPerl Objects Are Usually Hashes; Arrow Notation (->); Gene1: An Example of a Perl Class; Details of the Gene1 Class; Variable Names and Conventions; Carp and croak; The new Constructor Method; Creating an Object with bless; Using ref to Report an Object's Class; Initialize an Object with an Anonymous Hash; Accessor Methods; Gene2.pm: A Second Example of a Perl Class; Closures; Tracking Class Data from the Constructor Method; Accessor and Mutator Methods; Gene3.pm: A Third Example of a Perl Class; Testing Gene3.pm; How AUTOLOAD Works
- Defining Global VariablesAUTOLOAD Simplifies Writing Methods; Bypassing use strict; AUTOLOAD arguments; Using naming conventions to write code: get_ and set_; AUTOLOAD accessors; AUTOLOAD mutators; AUTOLOAD speedup; Cleaning Up Unused Objects with DESTROY; Gene.pm: A Fourth Example of a Perl Class; Building Gene.pm; Defining Attributes and Their Behaviors; Initializing the Attributes of a New Object; The newer new constructor; The clone constructor; Permissions; Gene.pm Test Program and Output; How to Document a Perl Class with POD; Additional Topics; Using Class::Struct to Define Classes
- Class Inheritance
