Bio/Cluster/FamilyI.pm

   1 #
   2 # BioPerl module for Bio::Cluster::FamilyI
   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::Cluster::FamilyI - Family 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 =head1 DESCRIPTION
  28
  29 This interface if for a Family object representing a family of
  30 biological objects. A generic implementation for this may be
  31 found a L<Bio::Cluster::Family>.
  32
  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://github.com/bioperl/bioperl-live/issues
  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 package Bio::Cluster::FamilyI;
  77 use strict;
  78
  79
  80 use base qw(Bio::ClusterI);
  81
  82 =head2 new
  83
  84   We don't mandate but encourage implementors to support at least the
  85   following named parameters upon object initialization.
  86
  87  Arguments          Description
  88  ---------          -----------
  89  -family_id         the name of the family
  90  -description       the consensus description of the family
  91  -annotation_score  the confidence by which the consensus description is
  92                     representative of the family
  93  -members           the members belonging to the family
  94  -alignment         the multiple alignment of the members
  95
  96 =cut
  97
  98
  99 =head2 family_id
 100
 101  Title   : family_id
 102  Usage   : Bio::Cluster::FamilyI->family_id("znfp");
 103  Function: get/set for the family id
 104  Returns : the family id
 105  Args    : the family id
 106
 107 =cut
 108
 109 sub family_id{
 110     shift->throw_not_implemented();
 111 }
 112
 113 =head2 family_score
 114
 115  Title   : family_score
 116  Usage   : Bio::Cluster::FamilyI->family_score(95);
 117  Function: get/set for the score of algorithm used to generate
 118            the family if present
 119  Returns : the score
 120  Args    : the score
 121
 122 =cut
 123
 124 sub family_score {
 125     shift->throw_not_implemented();
 126 }
 127
 128
 129 =head1 Methods inherited from L<Bio::ClusterI>
 130
 131 =cut
 132
 133 =head2 display_id
 134
 135  Title   : display_id
 136  Usage   :
 137  Function: Get the display name or identifier for the cluster
 138  Returns : a string
 139  Args    :
 140
 141 =cut
 142
 143 =head2 get_members
 144
 145  Title   : get_members
 146  Usage   : Bio::Cluster::FamilyI->get_members();
 147  Function: get the members of the family
 148  Returns : the array of members
 149  Args    : the array of members
 150
 151 =cut
 152
 153 =head2 description
 154
 155  Title   : description
 156  Usage   : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
 157  Function: get/set for the description of the family
 158  Returns : the description
 159  Args    : the description
 160
 161 =cut
 162
 163
 164 =head2 size
 165
 166  Title   : size
 167  Usage   : Bio::Cluster::FamilyI->size();
 168  Function: get/set for the description of the family
 169  Returns : size
 170  Args    :
 171
 172 =cut
 173
 174 =head2 cluster_score
 175
 176  Title   : cluster_score
 177  Usage   : $cluster ->cluster_score(100);
 178  Function: get/set for cluster_score which
 179            represent the score in which the clustering
 180            algorithm assigns to this cluster.
 181  Returns : a number
 182
 183 =cut
 184
 185 1;