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Bio::Factory::AnalysisI - An interface to analysis tool factory


This is an interface module - you do not instantiate it. Use Bio::Tools::Run::AnalysisFactory module:

  use Bio::Tools::Run::AnalysisFactory;
  my $list = Bio::Tools::Run::AnalysisFactory->new->available_analyses;


This interface contains all public methods for showing available analyses and for creating objects representing them.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:


Martin Senger (


Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.


This software is provided "as is" without warranty of any kind.




This is actually the main documentation...

If you try to call any of these methods directly on this Bio::Factory::AnalysisI object you will get a not implemented error message. You need to call them on a Bio::Tools::Run::AnalysisFactory object instead.


 Usage   : $factory->available_categories;
 Returns : an array reference with the names of
           available categories
 Args    : none

The analysis tools may be grouped into categories by their functional similarity, or by the similar data types they deal with. This method shows all available such categories.


 Usage   : $factory->available_analyses;
           $factory->available_analyses ($category);
 Returns : an array reference with the names of
           all available analyses, or the analyses
           available in the given '$category'
 Args    : none || category_name

Show available analyses. Their names usually consist of category analysis names, separated by ::.


 Usage   : $factory->create_analysis ($name);
 Returns : a Bio::Tools::Run::Analyis object
 Args    : analysis name

A real factory method creating an analysis object. The created object gets all access and location information from the factory object.