Bio::EnsEMBL::Funcgen ArrayChip
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Summary
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.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Funcgen::Storable
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Funcgen::Storable
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?
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.
Methods
array_idDescriptionCode
design_idDescriptionCode
get_ArrayDescriptionCode
nameDescriptionCode
newDescriptionCode
Methods description
array_idcode    nextTop
  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
design_idcodeprevnextTop
  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
get_ArraycodeprevnextTop
  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
namecodeprevnextTop
  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
newcodeprevnextTop
  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
Methods code
array_iddescriptionprevnextTop
sub array_id {
  my $self = shift;
  $self->{'array_id'} = shift if @_;
  return $self->{'array_id'};
}
design_iddescriptionprevnextTop
sub design_id {
  my $self = shift;
  $self->{'design_id'} = shift if @_; 
  return $self->{'design_id'};
}
get_ArraydescriptionprevnextTop
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;
}
namedescriptionprevnextTop
sub name {
  my $self = shift;
  $self->{'name'} = shift if @_;
  return $self->{'name'};
}
newdescriptionprevnextTop
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;
}
General documentation
AUTHORTop
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
CONTACTTop
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk