Bio/Factory/AnalysisI.pm

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