3 # BioPerl module for Bio::PopGen::GenotypeI
5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
7 # Cared for by Jason Stajich <jason-at-bioperl.org>
9 # Copyright Jason Stajich
11 # You may distribute this module under the same terms as perl itself
13 # POD documentation - main docs before the code
17 Bio::PopGen::GenotypeI - A marker and alleles for a specific individual
21 Give standard usage here
25 Describe the interface here
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.
35 bioperl-l@bioperl.org - General discussion
36 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
40 Please direct usage questions or support issues to the mailing list:
42 I<bioperl-l@bioperl.org>
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.
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
55 https://redmine.open-bio.org/projects/bioperl/
57 =head1 AUTHOR - Jason Stajich
59 Email jason-at-bioperl.org
63 The rest of the documentation details each of the object methods.
64 Internal methods are usually preceded with a _
69 # Let the code begin...
72 package Bio
::PopGen
::GenotypeI
;
76 use base
qw(Bio::Root::RootI);
81 Usage : my $name = $genotype->marker_name();
82 Function: Get the marker name for a genotype result
91 $self->throw_not_implemented();
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
110 $self->throw_not_implemented();
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
127 $self->throw_not_implemented();
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)
143 $self->throw_not_implemented();