# $Id $
#
# BioPerl module for Bio::PopGen::IndividualI
#
# 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::IndividualI - An individual who has Genotype or Sequence Results
=head1 SYNOPSIS
# Get a Bio::PopGen::IndividualI somehow
# test if it has alleles/genotypes for a given marker
if( $ind->has_marker($markername) ) {
}
# get the unique id
print $ind->unique_id, "\n";
# get the number of results (genotypes)
print $ind->num_results;
=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://redmine.open-bio.org/projects/bioperl/
=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::IndividualI;
use strict;
use base qw(Bio::Root::RootI);
=head2 unique_id
Title : unique_id
Usage : my $id = $individual->unique_id
Function: Unique Identifier
Returns : string representing unique identifier
Args : string
=cut
sub unique_id{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 num_genotypes
Title : num_genotypes
Usage : my $count = $person->num_results;
Function: returns the count of the number of Results for a person
Returns : integer
Args : none
=cut
sub num_genotypes {
shift->throw_not_implemented;
}
sub num_of_results{
my $self = shift;
$self->deprecated("num_of_results is deprecated, use num_genotypes instead");
$self->num_genotypes;
}
=head2 annotation
Title : annotation
Usage : my $annotation_collection = $ind->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this individual
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
=cut
sub annotation{
my ($self, $arg) = @_;
$self->throw_not_implemented();
}
=head2 get_Genotypes
Title : get_Genotypes
Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername);
Function: Get the genotypes for an individual, based on a criteria
Returns : Array of genotypes
Args : either none (return all genotypes) or
-marker => name of marker to return (exact match, case matters)
=cut
sub get_Genotypes{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 has_Marker
Title : has_Marker
Usage : if( $ind->has_Marker($name) ) {}
Function: Boolean test to see if an Individual has a genotype
for a specific marker
Returns : Boolean (true or false)
Args : String representing a marker name
=cut
sub has_Marker{
my ($self,$name) = @_;
$self->throw_not_implemented();
}
=head2 get_marker_names
Title : get_marker_names
Usage : my @names = $individual->get_marker_names;
Function: Returns the list of known marker names
Returns : List of strings
Args : none
=cut
sub get_marker_names{
my ($self) = @_;
$self->throw_not_implemented();
}
1;