What Bio::Factory Is In Bioperl

Question

[litiancheng.gansu]

I'm studying bioperl recently, but I don't know factory in bioperl, what does it do? could anyone help me to understand it?

Answer 1

[Neilfws]

Factories are not specific to Bioperl, nor to Perl. They are a design pattern, used in object-oriented programming (OOP).

If you know something about OOP, you'll know that an object is an instance of a class and creation of an object is termed instantiation. However, there are situations where objects can be similar in structure, but not identical (i.e. not simple instances of one class). In this situation, what you want is a subclass suited to the particular object and data that you have. This is a factory.

In Bioperl for example, we have Bio::Factory::EMBOSS. This provides factories to create objects for running programs from the EMBOSS suite and parsing their output. Many of these programs have similar, but not identical command line switches and data inputs/outputs - hence the need for factories. Similarly there are "sequence factories", for dealing with different sequence formats.

These links may be helpful:

• Wikipedia - Factory method pattern
• When should I use a factory to wrap a constructor in Perl?
• Factory Object
• Factory method example - Perl
• Perl Design Patterns, Part 3