Packages Modules Packages and Modules T. M. Murali Jan 17, 2005 T. M. Murali: Packages and Modules Packages Modules Reason for Packages I First step in good software design. I How do you protect different pieces of code from inadvertently tampering with each others variables? I Each named variable and named subroutine belongs to a particular package. I Default package is main. I Different packages can have variables/subroutines with the same name. I Each package has its own symbol table or namespace. T. M. Murali: Packages and Modules Packages Modules Declaring Packages I Package declaration: I package <name>; I Changes namespace until another package declaration or until the end of the current block, file, subroutine, or eval. I Say package main; to go back to main package. I Ability to assess the algorithm/data structure needed to solve a problem. I Ability to implement a small software system in Perl to solve bioinformatics tasks. T. M. Murali: Packages and Modules Packages Modules Referring to Variables in Another Package I Prefix variable/subroutine name with name of the package. I $Expression::number_of_genes I Expression::Cluster::k_means() I $::number_of_genes ≡$main::number_of_genes I The identifier ($, @, %) comes before the name of the package. I No package name means that you are accessing a variable in the current package. I Good design dictates that we should only access the subroutines in another package. I There is no relationship between the Expression and Expression::Cluster packages. T. M. Murali: Packages and Modules Packages Modules Lexical Variables I Defined using my. I Do not belong to a package’s namespace. I Scope is within the block that the variable is defined. I Variable is not visible to any subroutines that are called. I Scope can cross package boundaries. T. M. Murali: Packages and Modules Packages Modules Perl’s Module System I Package code into a separate file. I Put the file in a well-defined place. I Allow the compiler to add the file into other programmes semi-automatically. I Read perlmod and perlmodlib documentation for gory details. T. M. Murali: Packages and Modules Packages Modules Perl Module I A Perl module is a file with the .pm suffix that contains some Perl code. I Fundamental unit of code reuse. I Typically, one module contains one package. I Reuse a module with the use <module name>; statement. I use statement causes compiler to look for the corresponding module in a set of pre-defined locations, find the matching file, and evals (parse and executes) the code in that file. I Module name is related to the file name: the module Gene::Expression::Cluster is in the file Gene/Expression/Cluster.pm. T. M. Murali: Packages and Modules Packages Modules Setting Up the Gene::Expression::Cluster Module I Choose a standard directory, for example, /home/murali/lib/perl5. I Tell Perl about this directory: I (in tcsh) setenv PERL5LIB {$PERL5LIB}:/home/murali/lib/perl5 I (in the file that will use a module) I BEGIN { push(@INC, "/home/murali/lib/perl5"); } I use lib "/home/murali/lib/perl5"; I Create the Gene and Gene/Expression subdirectories in /home/murali/lib/perl5. I Create the file Cluster.pm in the Gene/Expression subdirectory. I Insert your code in Cluster.pm. I Add a statement that evaluates to true at the end of file, e.g. 1; I Now any programme can access this module with the statement use Gene::Expression::Cluster; T. M. Murali: Packages and Modules Packages Modules Exporting Subroutines I How does the code useing a module access the module’s subroutines? I By using the fully-qualified name, e.g., Gene::Expression::Cluster::k_means(); I Without using the fully-qualified name if the module exports the subroutine. I require Exporter; I our @ISA = ("Exporter"); I our @EXPORT = (k_means, hierarchical, bicluster); I See Programming Perl, Chapter 11, for use of @EXPORT_OK and @EXPORT_TAGS. I We will very rarely export variables in this class. I Once we start object-oriented Perl, we will very rarely export variables or subroutines from classes, since exporting violates the principle of encapsulation. T. M. Murali: Packages and Modules Packages Modules Autoloading I How does a module handle a call to an undefined subroutine in that module? I Before issuing a fatal error, Perl attempts to call the module’s AUTOLOAD subroutine. I Perl calls AUTOLOAD with the same arguments passed to the unimplemented subroutine. I Within AUTOLOAD, the special variable $AUTOLOAD contains the fully-qualified name of the subroutine. I AUTOLOAD can now decide what to do based on the value in $AUTOLOAD. I AUTOLOAD is especially useful in object-oriented programming. T. M. Murali: Packages and Modules Packages Modules The CPAN I The CPAN is the Comprehensive Perl Archive Network at http://www.cpan.org I Contains Perl modules, scripts, binary distributions, source code, documentation. I Explore it by hand. I Search it at http://search.cpan.org T. M. Murali: Packages and Modules Packages Modules Installing Code from CPAN I perl -MCPAN -e shell; I install Clone; I That is it! (If there are no errors ...). T. M. Murali: Packages and Modules.