Bio::Phylo::Factory - Creator of objects, reduces hardcoded class names in code
use Bio::Phylo::Factory; my $fac = Bio::Phylo::Factory->new; my $node = $fac->create_node( '-name' => 'node1' ); # probably prints 'Bio::Phylo::Forest::Node'? print ref $node;
The factory module is used to create other objects without having to 'use' their classes. This allows for greater flexibility in Bio::Phylo's design, as class names are no longer hard-coded all over the place.
Factory constructor.
Type : Constructor Title : new Usage : my $fac = Bio::Phylo::Factory->new; Function: Initializes a Bio::Phylo::Factory object. Returns : A Bio::Phylo::Factory object. Args : (optional) a hash keyed on short names, with class names for values. For example, 'node' => 'Bio::Phylo::Forest::Node', which will allow you to subsequently call $fac->create_node, which will return a Bio::Phylo::Forest::Node object. (Note that this example is enabled by default, so you don't need to specify it.)
Type : Factory methods Title : create Usage : my $foo = $fac->create('Foo::Class'); Function: Creates an instance of $class, with constructor arguments %args Returns : A Bio::Phylo::* object. Args : $class, a class name (required), %args, constructor arguments (optional)
Registers the argument class name such that subsequently the factory can instantiates objects of that class. For example, if you register Foo::Bar, the factory will be able to instantiate objects through the create_bar() method.
Type : Factory methods Title : register_class Usage : $fac->register_class('Foo::Bar'); Function: Registers a class name for instantiation Returns : Invocant Args : $class, a class name (required), or 'bar' => 'Foo::Bar', such that you can subsequently call $fac->create_bar()
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.