Bio/ClusterI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::ClusterI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
   8 #
   9 # Copyright Shawn Hoon
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::ClusterI - Cluster Interface
  18
  19 =head1 SYNOPSIS
  20
  21     # see the implementations of this interface for details
  22
  23     my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
  24                                -members    =>[$seq1,$seq2]);
  25     my @members = $cluster->get_members();
  26     my @sub_members = $cluster->get_members(-species=>"homo sapiens");
  27
  28
  29 =head1 DESCRIPTION
  30
  31 This interface is the basic structure for a cluster of bioperl objects.
  32 In this case it is up to the implementer to check arguments
  33 and initialize whatever new object the implementing class is designed for.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 L<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 of the bugs and their resolution. Bug reports can be submitted via the
  61 web:
  62
  63   http://bugzilla.open-bio.org/
  64
  65 =head1 AUTHOR - Shawn Hoon
  66
  67 Email shawnh@fugu-sg.org
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods.
  72 Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79 package Bio::ClusterI;
  80 use strict;
  81
  82
  83 use base qw(Bio::Root::RootI);
  84
  85 =head1 Implementation Specific Functions
  86
  87 These functions are the ones that a specific implementation must
  88 define.
  89
  90 =head2 new
  91
  92   We dont mandate but encourage implementors to support at least the
  93   following named parameters upon object initialization.
  94
  95   Argument        Description
  96   --------        -----------
  97   -display_id     the display ID or name for the cluster
  98   -description    the consensus description or name of the cluster
  99   -members        the array of objects belonging to the family
 100
 101 =cut
 102
 103 =head2 display_id
 104
 105  Title   : display_id
 106  Usage   :
 107  Function: Get the display name or identifier for the cluster
 108  Returns : a string
 109  Args    :
 110
 111 =cut
 112
 113 sub display_id{
 114     shift->throw_not_implemented();
 115 }
 116
 117
 118 =head2 description
 119
 120  Title   : description
 121  Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
 122  Function: get/set for the consensus description of the cluster
 123  Returns : the description string
 124  Args    : Optional the description string
 125
 126 =cut
 127
 128 sub description{
 129     shift->throw_not_implemented();
 130 }
 131
 132 =head2 size
 133
 134  Title   : size
 135  Usage   : Bio::ClusterI->size();
 136  Function: get/set for the size of the family,
 137            calculated from the number of members
 138  Returns : the size of the family
 139  Args    :
 140
 141 =cut
 142
 143 sub size {
 144     shift->throw_not_implemented();
 145 }
 146
 147 =head2 cluster_score
 148
 149  Title   : cluster_score
 150  Usage   : $cluster ->cluster_score(100);
 151  Function: get/set for cluster_score which
 152            represent the score in which the clustering
 153            algorithm assigns to this cluster.
 154  Returns : a number
 155
 156 =cut
 157
 158 sub cluster_score{
 159     shift->throw_not_implemented();
 160 }
 161
 162 =head2 get_members
 163
 164  Title   : get_members
 165  Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
 166  Function: retrieve the members of the family by some criteria, for
 167            example :
 168            $cluster->get_members(-species => 'homo sapiens');
 169
 170            Will return all members if no criteria are provided.
 171
 172  Returns : the array of members
 173  Args    :
 174
 175 =cut
 176
 177 sub get_members {
 178     shift->throw_not_implemented();
 179 }
 180
 181 1;