Bio/Factory/AnalysisI.pm

   1 #
   2 # BioPerl module for Bio::Factory::AnalysisI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Martin Senger <martin.senger@gmail.com>
   7 # For copyright and disclaimer see below.
   8 #
   9
  10 # POD documentation - main docs before the code
  11
  12 =head1 NAME
  13
  14 Bio::Factory::AnalysisI - An interface to analysis tool factory
  15
  16 =head1 SYNOPSIS
  17
  18 This is an interface module - you do not instantiate it.
  19 Use I<Bio::Tools::Run::AnalysisFactory> module:
  20
  21   use Bio::Tools::Run::AnalysisFactory;
  22   my $list = Bio::Tools::Run::AnalysisFactory->new->available_analyses;
  23
  24 =head1 DESCRIPTION
  25
  26 This interface contains all public methods for showing available
  27 analyses and for creating objects representing them.
  28
  29 =head1 FEEDBACK
  30
  31 =head2 Mailing Lists
  32
  33 User feedback is an integral part of the evolution of this and other
  34 Bioperl modules. Send your comments and suggestions preferably to
  35 the Bioperl mailing list.  Your participation is much appreciated.
  36
  37   bioperl-l@bioperl.org                  - General discussion
  38   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  39
  40 =head2 Support
  41
  42 Please direct usage questions or support issues to the mailing list:
  43
  44 I<bioperl-l@bioperl.org>
  45
  46 rather than to the module maintainer directly. Many experienced and
  47 reponsive experts will be able look at the problem and quickly
  48 address it. Please include a thorough description of the problem
  49 with code and data examples if at all possible.
  50
  51 =head2 Reporting Bugs
  52
  53 Report bugs to the Bioperl bug tracking system to help us keep track
  54 of the bugs and their resolution. Bug reports can be submitted via the
  55 web:
  56
  57   https://github.com/bioperl/bioperl-live/issues
  58
  59 =head1 AUTHOR
  60
  61 Martin Senger (martin.senger@gmail.com)
  62
  63 =head1 COPYRIGHT
  64
  65 Copyright (c) 2003, Martin Senger and EMBL-EBI.
  66 All Rights Reserved.
  67
  68 This module is free software; you can redistribute it and/or modify
  69 it under the same terms as Perl itself.
  70
  71 =head1 DISCLAIMER
  72
  73 This software is provided "as is" without warranty of any kind.
  74
  75 =head1 SEE ALSO
  76
  77 =over
  78
  79 =item *
  80
  81 http://www.ebi.ac.uk/Tools/webservices/soaplab/guide
  82
  83 =back
  84
  85 =head1 APPENDIX
  86
  87 This is actually the main documentation...
  88
  89 If you try to call any of these methods directly on this
  90 C<Bio::Factory::AnalysisI> object you will get a I<not implemented>
  91 error message. You need to call them on a
  92 C<Bio::Tools::Run::AnalysisFactory> object instead.
  93
  94 =cut
  95
  96
  97 # Let the code begin...
  98
  99 package Bio::Factory::AnalysisI;
 100 use strict;
 101
 102 use base qw(Bio::Root::RootI);
 103
 104
 105 # -----------------------------------------------------------------------------
 106
 107 =head2 available_categories
 108
 109  Usage   : $factory->available_categories;
 110  Returns : an array reference with the names of
 111            available categories
 112  Args    : none
 113
 114 The analysis tools may be grouped into categories by their functional
 115 similarity, or by the similar data types they deal with. This method
 116 shows all available such categories.
 117
 118 =cut
 119
 120 sub available_categories { shift->throw_not_implemented(); }
 121
 122 # -----------------------------------------------------------------------------
 123
 124 =head2 available_analyses
 125
 126  Usage   : $factory->available_analyses;
 127            $factory->available_analyses ($category);
 128  Returns : an array reference with the names of
 129            all available analyses, or the analyses
 130            available in the given '$category'
 131  Args    : none || category_name
 132
 133 Show available analyses. Their names usually consist of category
 134 analysis names, separated by C<::>.
 135
 136 =cut
 137
 138 sub available_analyses { shift->throw_not_implemented(); }
 139
 140 # -----------------------------------------------------------------------------
 141
 142 =head2 create_analysis
 143
 144  Usage   : $factory->create_analysis ($name);
 145  Returns : a Bio::Tools::Run::Analyis object
 146  Args    : analysis name
 147
 148 A real I<factory> method creating an analysis object. The created
 149 object gets all access and location information from the factory
 150 object.
 151
 152 =cut
 153
 154 sub create_analysis { shift->throw_not_implemented(); }
 155
 156 # -----------------------------------------------------------------------------
 157
 158
 159 1;
 160 __END__
 161