Raw content of Bio::EnsEMBL::Funcgen::ArrayChip
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# Ensembl module for Bio::EnsEMBL::Funcgen::ArrayChip
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::ArrayChip - A simple module to represent the concept/template of
a chip/slide within an array, of which the physical manifestation is an ExperimentalChip.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::ArrayChip;
my $ec = Bio::EnsEMBL::Funcgen::ArrayChip->new(
-ARRAY_ID => $array->dbID(),
-NAME => $desc,
-DESIGN_ID => $design_id,
);
#add more methods here?
=head1 DESCRIPTION
An ArrayChip object represent the concept of an array chip/slide withing a given array/chipset.
The data for ArrayChips is stored in the array_chip table.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::ArrayChip;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Funcgen::Storable;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
=head2 new
Arg [-ARRAY_ID] : int - the dbID of the parent array
Arg [-DESIGN_ID] : string - the unqiue deisng ID defined by the array vendor
Arg [-NAME] : string - the name of the array chip
Example : my $array_chip = Bio::EnsEMBL::Funcgen::ArrayChip->new(
-ARRAY_ID => $array->dbID(),
-NAME => $desc,
-DESIGN_ID => $design_id,
); );
Description: Creates a new Bio::EnsEMBL::Funcgen::ArrayChip object.
Returntype : Bio::EnsEMBL::Funcgen::ArrayChip
Exceptions : None ? should throw if mandaotry params not set
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($array_id, $name, $design_id)
= rearrange( ['ARRAY_ID', 'NAME', 'DESIGN_ID'], @_ );
throw("Must define a name($name) and design_id($design_id)") if(! $name || ! $design_id);
#mandatory params all but design_id?
$self->array_id($array_id) if defined $array_id;
$self->name($name);
$self->design_id($design_id);
return $self;
}
=head2 array_id
Arg [1] : (optional) int - the parent array dbID
Example : my $array_id = $array_chip->array_id();
Description: Getter, setter array_id attribute.
Returntype : int
Exceptions : None
Caller : General
Status : At Risk
=cut
sub array_id {
my $self = shift;
$self->{'array_id'} = shift if @_;
return $self->{'array_id'};
}
=head2 name
Arg [1] : (optional) string - the array chip name
Example : my $ac_name = $array_chip->name();
Description: Getter, setter for the name attribute
Returntype : string
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if @_;
return $self->{'name'};
}
=head2 design_id
Arg [1] : (optional) string - the array_chip unique design id as deinfed by the array vendor
Example : my $design_id = $array_chip->design_id();
Description: Getter, setter for the design_id attribute
Returntype : string
Exceptions : None
Caller : General
Status : At Risk
=cut
sub design_id {
my $self = shift;
$self->{'design_id'} = shift if @_;
return $self->{'design_id'};
}
=head2 get_Array
Example : my $array = $array_chip->get_array();
Description: Getter for the array attribute
Returntype : Bio::EnsEMBL::Funcgen::Array
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_Array {
my $self = shift;
if(! defined $self->{'array'}){
$self->{'array'} = $self->adaptor->db->get_ArrayAdaptor()->fetch_by_dbID($self->array_id());
}
return $self->{'array'};
}
1;
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