Raw content of Bio::EnsEMBL::Variation::VariationGroup
<![CDATA[# Ensembl module for Bio::EnsEMBL::Variation::VariationGroup
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Variation::VariationGroup - Ensembl representation of a grouping of
variations (aka haplotype set).
=head1 SYNOPSIS
use Bio::EnsEMBL::Variation::VariationGroup;
...
=head1 DESCRIPTION
This is a class representing a grouping of variations that have tight linkage.
This is commonly known as a Haplotype Set. It can be viewed as a vertical
grouping of AlleleGroups.
=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::VariationGroup;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [dbID] :
int - unique internal identifier for this allele group
Arg [ADAPTOR] :
Bio::EnsEMBL::Variation::DBSQL::VariationGroupAdaptor
Arg [NAME] :
string - the name of this variation group
Arg [SOURCE] :
string - the name of the database this variation group is from
Arg [TYPE] :
string - the type of this group. Must be either 'haplotype' or 'tag'.
Arg [VARIATIONS] :
reference to list of Bio::EnsEMBL::Variation::Variation objects - the
variations which make up this variation group.
Example :
$ag = Bio::EnsEMBL::Variation::VariationGroup->new
(-name => 'PERLEGEN:B000007',
-source => 'dbSNP',
-type => 'haplotype',
-variations => [$var1, $var2, $var3, $var4]);
Description: Constructor. Instantiates a new VariationGroup
Returntype : Bio::EnsEMBL::Variation::VariationGroup
Exceptions : none
Caller : general
Status : At Risk
=cut
sub new {
my $class = shift;
my ($dbID, $adaptor, $name, $type, $src, $vars) =
rearrange([qw(DBID ADAPTOR NAME TYPE SOURCE VARIATIONS)], @_);
if(defined($vars) && !ref($vars) eq 'ARRAY') {
throw("Reference to list of Bio::EnsEMBL::Variation::Variation ".
"objects expected");
}
$vars ||= [];
return bless {'dbID' => $dbID,
'adaptor' => $adaptor,
'name' => $name,
'type' => $type,
'source' => $src,
'variations' => $vars}, $class;
}
=head2 name
Arg [1] : string $name
Example : print $allele_group->name();
Description: Getter/Setter for the name of this VariationGroup
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if(@_);
return $self->{'name'};
}
=head2 source
Arg [1] : (optional) string $source
Example : print $ag->source(), "\n";
Description: Getter/Setter for the name of the source database of this
VariationGroup.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub source {
my $self = shift;
$self->{'source'} = shift if(@_);
return $self->{'source'};
}
=head2 type
Arg [1] : string $newval (optional)
The new value to set the type attribute to
Example : $type = $vg->type()
Description: Getter/Setter for the type attribute
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub type{
my $self = shift;
return $self->{'type'} = shift if(@_);
return $self->{'type'};
}
=head2 get_all_Variations
Arg [1] : none
Example :
Description: Retrieves all variations that make up this VariationGroup.
Returntype : reference to a list of strings
Exceptions : none
Caller : general
Status : At Risk
=cut
sub get_all_Variations {
my $self = shift;
return $self->{'variations'};
}
=head2 add_Variation
Arg [1] : Bio::EnsEMBL::Variation::Variation $var
Example : $vg->add_Variation($var2);
Description: Adds a Variation to this VariationGroup
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
Status : At Risk
=cut
sub add_Variation {
my $self = shift;
my $var = shift;
if(!ref($var) || !$var->isa('Bio::EnsEMBL::Variation::Variation')) {
throw('Bio::EnsEMBL::Variation::Variation argument expected');
}
push @{$self->{'variations'}}, $var;
return;
}
1;
]]>