3 # BioPerl module for Bio::Factory::AnalysisI
5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
7 # Cared for by Martin Senger <martin.senger@gmail.com>
8 # For copyright and disclaimer see below.
11 # POD documentation - main docs before the code
15 Bio::Factory::AnalysisI - An interface to analysis tool factory
19 This is an interface module - you do not instantiate it.
20 Use I<Bio::Tools::Run::AnalysisFactory> module:
22 use Bio::Tools::Run::AnalysisFactory;
23 my $list = Bio::Tools::Run::AnalysisFactory->new->available_analyses;
27 This interface contains all public methods for showing available
28 analyses and for creating objects representing them.
34 User feedback is an integral part of the evolution of this and other
35 Bioperl modules. Send your comments and suggestions preferably to
36 the Bioperl mailing list. Your participation is much appreciated.
38 bioperl-l@bioperl.org - General discussion
39 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
43 Please direct usage questions or support issues to the mailing list:
45 I<bioperl-l@bioperl.org>
47 rather than to the module maintainer directly. Many experienced and
48 reponsive experts will be able look at the problem and quickly
49 address it. Please include a thorough description of the problem
50 with code and data examples if at all possible.
54 Report bugs to the Bioperl bug tracking system to help us keep track
55 of the bugs and their resolution. Bug reports can be submitted via the
58 http://bugzilla.open-bio.org/
62 Martin Senger (martin.senger@gmail.com)
66 Copyright (c) 2003, Martin Senger and EMBL-EBI.
69 This module is free software; you can redistribute it and/or modify
70 it under the same terms as Perl itself.
74 This software is provided "as is" without warranty of any kind.
82 http://www.ebi.ac.uk/Tools/webservices/soaplab/guide
88 This is actually the main documentation...
90 If you try to call any of these methods directly on this
91 C<Bio::Factory::AnalysisI> object you will get a I<not implemented>
92 error message. You need to call them on a
93 C<Bio::Tools::Run::AnalysisFactory> object instead.
98 # Let the code begin...
100 package Bio
::Factory
::AnalysisI
;
103 use base
qw(Bio::Root::RootI);
106 # -----------------------------------------------------------------------------
108 =head2 available_categories
110 Usage : $factory->available_categories;
111 Returns : an array reference with the names of
115 The analysis tools may be grouped into categories by their functional
116 similarity, or by the similar data types they deal with. This method
117 shows all available such categories.
121 sub available_categories
{ shift->throw_not_implemented(); }
123 # -----------------------------------------------------------------------------
125 =head2 available_analyses
127 Usage : $factory->available_analyses;
128 $factory->available_analyses ($category);
129 Returns : an array reference with the names of
130 all available analyses, or the analyses
131 available in the given '$category'
132 Args : none || category_name
134 Show available analyses. Their names usually consist of category
135 analysis names, separated by C<::>.
139 sub available_analyses
{ shift->throw_not_implemented(); }
141 # -----------------------------------------------------------------------------
143 =head2 create_analysis
145 Usage : $factory->create_analysis ($name);
146 Returns : a Bio::Tools::Run::Analyis object
149 A real I<factory> method creating an analysis object. The created
150 object gets all access and location information from the factory
155 sub create_analysis
{ shift->throw_not_implemented(); }
157 # -----------------------------------------------------------------------------