Raw content of Bio::EnsEMBL::AffyArray =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;