Bio/ClusterI.pm

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