Raw content of Bio::EnsEMBL::AffyArray
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::AffyArray - A module to represent an Affymetrix array.
=head1 SYNOPSIS
use Bio::EnsEMBL::AffyArray;
my $array = Bio::EnsEMBL::AffyArray->new(
-NAME => 'Affy-1',
-INCLUDED_IN => $another_array,
-SETSIZE => 16,
);
=head1 DESCRIPTION
An AffyArray object represents an Affymetrix array. The data (currently
the name, probeset size and parent array) are stored in the oligo_array
table.
Each array can have a parent array (another array that contains all the
probes of this array). This is rarely (if ever) used.
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::AffyArray;
use Bio::EnsEMBL::OligoArray;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::OligoArray);
=head2 new
Arg [-NAME]:
string - the name of this array
Arg [-INCLUDED_IN]:
(optional) Bio::EnsEMBL::OligoArray - a possible superset array
Arg [-SETSIZE]:
int - the number of probes in a probe set
Example : my $array = Bio::EnsEMBL::AffyArray->new(
-NAME => 'Affy-1',
-INCLUDED_IN => $another_array,
-SETSIZE => 16,
);
Description: Creates a new Bio::EnsEMBL::AffyArray object.
Returntype : Bio::EnsEMBL::AffyArray
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
# All AffyArray objects are OligoArray objects of type AFFY
$self->type('AFFY');
return $self;
}
=head2 get_all_AffyProbes
Args : None
Example : my $probes = $array->get_all_AffyProbes();
Description: Returns all probes on an Affy array. Needs a database
connection.
Returntype : Listref of Bio::EnsEMBL::AffyProbe objects
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_all_AffyProbes {
my $self = shift;
return $self->get_all_Probes();
}
1;
]]>