# $Id $
#
# BioPerl module for Bio::PopGen::GenotypeI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::PopGen::GenotypeI - A marker and alleles for a specific individual
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the interface here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::PopGen::GenotypeI;
use strict;
use base qw(Bio::Root::RootI);
=head2 marker_name
Title : marker_name
Usage : my $name = $genotype->marker_name();
Function: Get the marker name for a genotype result
Returns : string
Args : none
=cut
sub marker_name{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 individual_id
Title : individual_id
Usage : my $indid = $genotype->individual_id();
Function: Gets the individual id associated with a genotype
This is effectively a back reference since we will typically
associate a genotype with an individual with an
individual HAS-A genotype relationship.
Returns : unique id string for an individual
Args : none
=cut
sub individual_id{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 annotation
Title : annotation
Usage : my $annotation_collection = $genotype->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this genotype
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
=cut
sub annotation{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 get_Alleles
Title : get_Alleles
Usage : my @alleles = $genotype->get_Alleles();
Function: Get the alleles for a given marker and individual
Returns : array of alleles (strings in many implementations)
Args : none
=cut
sub get_Alleles{
my ($self) = @_;
$self->throw_not_implemented();
}
1;