Bio/PopGen/GenotypeI.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::PopGen::GenotypeI
   4 #
   5 # Cared for by Jason Stajich <jason-at-bioperl.org>
   6 #
   7 # Copyright Jason Stajich
   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::PopGen::GenotypeI - A marker and alleles for a specific individual
  16
  17 =head1 SYNOPSIS
  18
  19 Give standard usage here
  20
  21 =head1 DESCRIPTION
  22
  23 Describe the interface here
  24
  25 =head1 FEEDBACK
  26
  27 =head2 Mailing Lists
  28
  29 User feedback is an integral part of the evolution of this and other
  30 Bioperl modules. Send your comments and suggestions preferably to
  31 the Bioperl mailing list.  Your participation is much appreciated.
  32
  33   bioperl-l@bioperl.org                  - General discussion
  34   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  35
  36 =head2 Reporting Bugs
  37
  38 Report bugs to the Bioperl bug tracking system to help us keep track
  39 of the bugs and their resolution. Bug reports can be submitted via
  40 email or the web:
  41
  42   http://bugzilla.open-bio.org/
  43
  44 =head1 AUTHOR - Jason Stajich
  45
  46 Email jason-at-bioperl.org
  47
  48 =head1 APPENDIX
  49
  50 The rest of the documentation details each of the object methods.
  51 Internal methods are usually preceded with a _
  52
  53 =cut
  54
  55
  56 # Let the code begin...
  57
  58
  59 package Bio::PopGen::GenotypeI;
  60 use strict;
  61
  62
  63 use base qw(Bio::Root::RootI);
  64
  65 =head2 marker_name
  66
  67  Title   : marker_name
  68  Usage   : my $name = $genotype->marker_name();
  69  Function: Get the marker name for a genotype result
  70  Returns : string
  71  Args    : none
  72
  73
  74 =cut
  75
  76 sub marker_name{
  77     my ($self) = @_;
  78     $self->throw_not_implemented();
  79 }
  80
  81 =head2 individual_id
  82
  83  Title   : individual_id
  84  Usage   : my $indid = $genotype->individual_id();
  85  Function: Gets the individual id associated with a genotype
  86            This is effectively a back reference since we will typically
  87            associate a genotype with an individual with an
  88            individual HAS-A genotype relationship.
  89  Returns : unique id string for an individual
  90  Args    : none
  91
  92
  93 =cut
  94
  95 sub individual_id{
  96    my ($self) = @_;
  97    $self->throw_not_implemented();
  98 }
  99
 100 =head2 get_Alleles
 101
 102  Title   : get_Alleles
 103  Usage   : my @alleles = $genotype->get_Alleles();
 104  Function: Get the alleles for a given marker and individual
 105  Returns : array of alleles (strings in many implementations)
 106  Args    : none
 107
 108
 109 =cut
 110
 111 sub get_Alleles{
 112    my ($self) = @_;
 113    $self->throw_not_implemented();
 114 }
 115
 116 1;