Bio/Cluster/FamilyI.pm

   1 #
   2 # BioPerl module for Bio::Cluster::FamilyI
   3 #
   4 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
   5 #
   6 # Copyright Shawn Hoon
   7 #
   8 # You may distribute this module under the same terms as perl itself
   9
  10 # POD documentation - main docs before the code
  11
  12 =head1 NAME
  13
  14 Bio::Cluster::FamilyI - Family Interface
  15
  16 =head1 SYNOPSIS
  17
  18     # see the implementations of this interface for details
  19
  20     my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
  21                                -members    =>[$seq1,$seq2]);
  22     my @members = $cluster->get_members();
  23     my @sub_members = $cluster->get_members(-species=>"homo sapiens");
  24
  25 =head1 DESCRIPTION
  26
  27 This interface if for a Family object representing a family of
  28 biological objects. A generic implementation for this may be
  29 found a L<Bio::Cluster::Family>.
  30
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Reporting Bugs
  44
  45 Report bugs to the Bioperl bug tracking system to help us keep track
  46 of the bugs and their resolution. Bug reports can be submitted via the
  47 web:
  48
  49   http://bugzilla.open-bio.org/
  50
  51 =head1 AUTHOR - Shawn Hoon
  52
  53 Email shawnh@fugu-sg.org
  54
  55 =head1 APPENDIX
  56
  57 The rest of the documentation details each of the object methods.
  58 Internal methods are usually preceded with a _
  59
  60 =cut
  61
  62
  63 package Bio::Cluster::FamilyI;
  64 use strict;
  65
  66
  67 use base qw(Bio::ClusterI);
  68
  69 =head2 new
  70
  71   We dont mandate but encourage implementors to support at least the
  72   following named parameters upon object initialization.
  73
  74  Arguments          Description
  75  ---------          -----------
  76  -family_id         the name of the family
  77  -description       the consensus description of the family
  78  -annotation_score  the confidence by which the consensus description is
  79                     representative of the family
  80  -members           the members belonging to the family
  81  -alignment         the multiple alignment of the members
  82
  83 =cut
  84
  85
  86 =head2 family_id
  87
  88  Title   : family_id
  89  Usage   : Bio::Cluster::FamilyI->family_id("znfp");
  90  Function: get/set for the family id
  91  Returns : the family id
  92  Args    : the family id
  93
  94 =cut
  95
  96 sub family_id{
  97     shift->throw_not_implemented();
  98 }
  99
 100 =head2 family_score
 101
 102  Title   : family_score
 103  Usage   : Bio::Cluster::FamilyI->family_score(95);
 104  Function: get/set for the score of algorithm used to generate
 105            the family if present
 106  Returns : the score
 107  Args    : the score
 108
 109 =cut
 110
 111 sub family_score {
 112     shift->throw_not_implemented();
 113 }
 114
 115
 116 =head1 Methods inherited from L<Bio::ClusterI>
 117
 118 =cut
 119
 120 =head2 display_id
 121
 122  Title   : display_id
 123  Usage   :
 124  Function: Get the display name or identifier for the cluster
 125  Returns : a string
 126  Args    :
 127
 128 =cut
 129
 130 =head2 get_members
 131
 132  Title   : get_members
 133  Usage   : Bio::Cluster::FamilyI->get_members();
 134  Function: get the members of the family
 135  Returns : the array of members
 136  Args    : the array of members
 137
 138 =cut
 139
 140 =head2 description
 141
 142  Title   : description
 143  Usage   : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
 144  Function: get/set for the description of the family
 145  Returns : the description
 146  Args    : the description
 147
 148 =cut
 149
 150
 151 =head2 size
 152
 153  Title   : size
 154  Usage   : Bio::Cluster::FamilyI->size();
 155  Function: get/set for the description of the family
 156  Returns : size
 157  Args    :
 158
 159 =cut
 160
 161 =head2 cluster_score
 162
 163  Title   : cluster_score
 164  Usage   : $cluster ->cluster_score(100);
 165  Function: get/set for cluster_score which
 166            represent the score in which the clustering
 167            algorithm assigns to this cluster.
 168  Returns : a number
 169
 170 =cut
 171
 172 1;