Bio/PopGen/GenotypeI.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::PopGen::GenotypeI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason-at-bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  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::PopGen::GenotypeI - A marker and alleles for a specific individual
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the interface here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 of the bugs and their resolution. Bug reports can be submitted via
  53 email or the web:
  54
  55   https://github.com/bioperl/bioperl-live/issues
  56
  57 =head1 AUTHOR - Jason Stajich
  58
  59 Email jason-at-bioperl.org
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object methods.
  64 Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68
  69 # Let the code begin...
  70
  71
  72 package Bio::PopGen::GenotypeI;
  73 use strict;
  74
  75
  76 use base qw(Bio::Root::RootI);
  77
  78 =head2 marker_name
  79
  80  Title   : marker_name
  81  Usage   : my $name = $genotype->marker_name();
  82  Function: Get the marker name for a genotype result
  83  Returns : string
  84  Args    : none
  85
  86
  87 =cut
  88
  89 sub marker_name{
  90     my ($self) = @_;
  91     $self->throw_not_implemented();
  92 }
  93
  94 =head2 individual_id
  95
  96  Title   : individual_id
  97  Usage   : my $indid = $genotype->individual_id();
  98  Function: Gets the individual id associated with a genotype
  99            This is effectively a back reference since we will typically
 100            associate a genotype with an individual with an
 101            individual HAS-A genotype relationship.
 102  Returns : unique id string for an individual
 103  Args    : none
 104
 105
 106 =cut
 107
 108 sub individual_id{
 109    my ($self) = @_;
 110    $self->throw_not_implemented();
 111 }
 112
 113
 114 =head2 annotation
 115
 116  Title   : annotation
 117  Usage   : my $annotation_collection = $genotype->annotation;
 118  Function: Get/set a Bio::AnnotationCollectionI for this genotype
 119  Returns : Bio::AnnotationCollectionI object
 120  Args    : [optional set] Bio::AnnotationCollectionI object
 121
 122
 123 =cut
 124
 125 sub annotation{
 126    my ($self) = @_;
 127    $self->throw_not_implemented();
 128 }
 129
 130 =head2 get_Alleles
 131
 132  Title   : get_Alleles
 133  Usage   : my @alleles = $genotype->get_Alleles();
 134  Function: Get the alleles for a given marker and individual
 135  Returns : array of alleles (strings in many implementations)
 136  Args    : none
 137
 138
 139 =cut
 140
 141 sub get_Alleles{
 142    my ($self) = @_;
 143    $self->throw_not_implemented();
 144 }
 145 1;