Raw content of Bio::EnsEMBL::Variation::Allele
<![CDATA[# Ensembl module for Bio::EnsEMBL::Variation::Allele
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Variation::Allele - A single allele of a nucleotide variation.
=head1 SYNOPSIS
$allele = Bio::EnsEMBL::Variation::Allele->new
(-allele => 'A',
-frequency => 0.85,
-population => $population);
$delete = Bio::EnsEMBL::Variation::Allele->new
(-allele => '-',
-frequency => 0.15,
-population => $population);
...
$astr = $a->allele();
$pop = $a->population();
$freq = $a->frequency();
print $a->allele();
if($a->populaton) {
print " found in population ", $allele->population->name();
}
if(defined($a->frequency())) {
print " with frequency ", $a->frequency();
}
print "\n";
=head1 DESCRIPTION
This is a class representing a single allele of a variation. In addition to
the nucleotide(s) (or absence of) that representing the allele frequency
and population information may be present.
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Variation::Allele;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
our @ISA = ('Bio::EnsEMBL::Storable');
=head2 new
Arg [-dbID]: int - unique internal identifier for the Allele
Arg [-ADAPTOR]: Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor
Arg [-ALLELE]: string - the nucleotide string representing the allele
Arg [-FREQUENCY]: float - the frequency of the allele
Arg [-POPULATION]: Bio::EnsEMBL::Variation::Population - the population
in which the allele was recorded
Example : $allele = Bio::EnsEMBL::Variation::Allele->new
(-allele => 'A',
-frequency => 0.85,
-population => $pop);
Description: Constructor. Instantiates a new Allele object.
Returntype : Bio::EnsEMBL::Variation::Allele
Exceptions : none
Caller : general
Status : At Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ($dbID, $adaptor, $allele, $freq, $pop) =
rearrange(['dbID', 'ADAPTOR', 'ALLELE', 'FREQUENCY', 'POPULATION'], @_);
return bless {'dbID' => $dbID,
'adaptor' => $adaptor,
'allele' => $allele,
'frequency' => $freq,
'population' => $pop}, $class;
}
=head2 allele
Arg [1] : string $newval (optional)
The new value to set the allele attribute to
Example : print $a->allele();
$a1->allele('A');
$a2->allele('-');
Description: Getter/Setter for the allele attribute. The allele is a string
of nucleotide sequence, or a '-' representing the absence of
sequence (deletion).
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub allele{
my $self = shift;
return $self->{'allele'} = shift if(@_);
return $self->{'allele'};
}
=head2 frequency
Arg [1] : float $newval (optional)
The new value to set the frequency attribute to
Example : $frequency = $a->frequency();
Description: Getter/Setter for the frequency attribute. The frequency is
the frequency of the occurance of the allele. If the population
attribute it is the frequency of the allele within that
population.
Returntype : float
Exceptions : none
Caller : general
Status : At Risk
=cut
sub frequency{
my $self = shift;
return $self->{'frequency'} = shift if(@_);
return $self->{'frequency'};
}
=head2 population
Arg [1] : Bio::EnsEMBL::Variation::Population $newval (optional)
The new value to set the population attribute to
Example : $population = $a->population();
Description: Getter/Setter for the population attribute
Returntype : Bio::EnsEMBL::Variation::Population
Exceptions : throw on incorrect argument
Caller : general
Status : At Risk
=cut
sub population{
my $self = shift;
if(@_) {
if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Population')) {
throw('Bio::EnsEMBL::Variation::Population argument expected.');
}
$self->{'population'} = shift;
}
return $self->{'population'};
}
1;
]]>