Bio/ClusterI.pm

   1 #
   2 # BioPerl module for Bio::ClusterI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
   7 #
   8 # Copyright Shawn Hoon
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::ClusterI - Cluster Interface
  17
  18 =head1 SYNOPSIS
  19
  20     # see the implementations of this interface for details
  21
  22     my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
  23                                -members    =>[$seq1,$seq2]);
  24     my @members = $cluster->get_members();
  25     my @sub_members = $cluster->get_members(-species=>"homo sapiens");
  26
  27
  28 =head1 DESCRIPTION
  29
  30 This interface is the basic structure for a cluster of bioperl objects.
  31 In this case it is up to the implementer to check arguments
  32 and initialize whatever new object the implementing class is designed for.
  33
  34 =head1 FEEDBACK
  35
  36 =head2 Mailing Lists
  37
  38 User feedback is an integral part of the evolution of this and other
  39 Bioperl modules. Send your comments and suggestions preferably to
  40 the Bioperl mailing list.  Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 of the bugs and their resolution. Bug reports can be submitted via the
  60 web:
  61
  62   https://redmine.open-bio.org/projects/bioperl/
  63
  64 =head1 AUTHOR - Shawn Hoon
  65
  66 Email shawnh@fugu-sg.org
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object methods.
  71 Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75
  76 # Let the code begin...
  77
  78 package Bio::ClusterI;
  79 use strict;
  80
  81
  82 use base qw(Bio::Root::RootI);
  83
  84 =head1 Implementation Specific Functions
  85
  86 These functions are the ones that a specific implementation must
  87 define.
  88
  89 =head2 new
  90
  91   We don't mandate but encourage implementors to support at least the
  92   following named parameters upon object initialization.
  93
  94   Argument        Description
  95   --------        -----------
  96   -display_id     the display ID or name for the cluster
  97   -description    the consensus description or name of the cluster
  98   -members        the array of objects belonging to the family
  99
 100 =cut
 101
 102 =head2 display_id
 103
 104  Title   : display_id
 105  Usage   :
 106  Function: Get the display name or identifier for the cluster
 107  Returns : a string
 108  Args    :
 109
 110 =cut
 111
 112 sub display_id{
 113     shift->throw_not_implemented();
 114 }
 115
 116
 117 =head2 description
 118
 119  Title   : description
 120  Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
 121  Function: get/set for the consensus description of the cluster
 122  Returns : the description string
 123  Args    : Optional the description string
 124
 125 =cut
 126
 127 sub description{
 128     shift->throw_not_implemented();
 129 }
 130
 131 =head2 size
 132
 133  Title   : size
 134  Usage   : Bio::ClusterI->size();
 135  Function: get/set for the size of the family,
 136            calculated from the number of members
 137  Returns : the size of the family
 138  Args    :
 139
 140 =cut
 141
 142 sub size {
 143     shift->throw_not_implemented();
 144 }
 145
 146 =head2 cluster_score
 147
 148  Title   : cluster_score
 149  Usage   : $cluster ->cluster_score(100);
 150  Function: get/set for cluster_score which
 151            represent the score in which the clustering
 152            algorithm assigns to this cluster.
 153  Returns : a number
 154
 155 =cut
 156
 157 sub cluster_score{
 158     shift->throw_not_implemented();
 159 }
 160
 161 =head2 get_members
 162
 163  Title   : get_members
 164  Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
 165  Function: retrieve the members of the family by some criteria, for
 166            example :
 167            $cluster->get_members(-species => 'homo sapiens');
 168
 169            Will return all members if no criteria are provided.
 170
 171  Returns : the array of members
 172  Args    :
 173
 174 =cut
 175
 176 sub get_members {
 177     shift->throw_not_implemented();
 178 }
 179
 180 1;