diff variant_effect_predictor/Bio/Factory/AnalysisI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Factory/AnalysisI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: AnalysisI.pm,v 1.2.2.1 2003/07/04 02:40:29 shawnh Exp $
+#
+# BioPerl module for Bio::Factory::AnalysisI
+#
+# Cared for by Martin Senger <[e-mail]>
+# For copyright and disclaimer see below.
+#
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Factory::AnalysisI - An interface to analysis tool factory
+
+=head1 SYNOPSIS
+
+This is an interface module - you do not instantiate it.
+Use I<Bio::Tools::Run::AnalysisFactory> module:
+
+  use Bio::Tools::Run::AnalysisFactory;
+  my $list = new Bio::Tools::Run::AnalysisFactory->available_analyses;
+
+=head1 DESCRIPTION
+
+This interface contains all public methods for showing available
+analyses and for creating objects representing them.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bioperl.org/bioperl-bugs/
+
+=head1 AUTHOR
+
+Martin Senger ([e-mail])
+
+=head1 COPYRIGHT
+
+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.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=head1 SEE ALSO
+
+=over
+
+=item *
+
+http://industry.ebi.ac.uk/soaplab/Perl_Client.html
+
+=back
+
+=head1 APPENDIX
+
+This is actually the main documentation...
+
+If you try to call any of these methods directly on this
+C<Bio::Factory::AnalysisI> object you will get a I<not implemented>
+error message. You need to call them on a
+C<Bio::Tools::Run::AnalysisFactory> object instead.
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::Factory::AnalysisI;
+use vars qw(@ISA $Revision);
+use strict;
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+BEGIN {
+    $Revision = q$Id: AnalysisI.pm,v 1.2.2.1 2003/07/04 02:40:29 shawnh Exp $;
+}
+
+
+# -----------------------------------------------------------------------------
+
+=head2 available_categories
+
+ 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.
+
+=cut
+
+sub available_categories { shift->throw_not_implemented(); }
+
+# -----------------------------------------------------------------------------
+
+=head2 available_analyses
+
+ 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 C<::>.
+
+=cut
+
+sub available_analyses { shift->throw_not_implemented(); }
+
+# -----------------------------------------------------------------------------
+
+=head2 create_analysis
+
+ Usage   : $factory->create_analysis ($name);
+ Returns : a Bio::Tools::Run::Analyis object
+ Args    : analysis name
+
+A real I<factory> method creating an analysis object. The created
+object gets all access and location information from the factory
+object.
+
+=cut
+
+sub create_analysis { shift->throw_not_implemented(); }
+
+# -----------------------------------------------------------------------------
+
+
+1;
+__END__
+