Bio::EnsEMBL::Funcgen CellType
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Summary
Bio::EnsEMBL::Funcgen::CellType - A module to represent a CellType.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Storable
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Storable
Synopsis
use Bio::EnsEMBL::Funcgen::CellType;
Description
This is a simple class to represent information about a CellType. This may represent an individual cell line or a more
generic tissue type.
Methods
descriptionDescriptionCode
display_labelDescriptionCode
nameDescriptionCode
newDescriptionCode
Methods description
descriptioncode    nextTop
  Arg [1]    : string - description
  Example    : my $desc = $ct->description();
  Description: Getter and setter of description attribute for CellType
               objects
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Low Risk
display_labelcodeprevnextTop
  Arg [1]    : (optional) string - description
  Example    : my $display_label = $ct->display_label();
  Description: Getter and setter of display_label attribute for CellType
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk
namecodeprevnextTop
  Arg [1]    : string - name
  Example    : my $name = $ct->name();
  Description: Getter and setter of name attribute for CellType
               objects
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Low Risk
newcodeprevnextTop
  Arg [-name]          : string - name of CellType
  Arg [-display_label] : string - display label of CellType
  #Arg [-type]          : string - type of cell i.e.  ???? or Tissue, LINE?? enum?
  ?? xref to coriell ??
  Example              : my $ct = Bio::EnsEMBL::Funcgen::CellType->new(
                                                               -name          => "U2OS",
                                                               -display_label => "",#?
                                                               -description   => "Human Bone Osteosarcoma Epithelial Cells",
                                                               #-type/class => "TISSUE", enum?
                                                               #xref/coriell id?
                                                                );
  Description: Constructor method for CellType class
  Returntype : Bio::EnsEMBL::Funcgen::CellType
  Exceptions : Throws if name and type not defined.
  Caller     : General
  Status     : At risk
Methods code
descriptiondescriptionprevnextTop
sub description {
    my $self = shift;
    $self->{'description'} = shift if @_;
    return $self->{'description'};
}
display_labeldescriptionprevnextTop
sub display_label {
    my $self = shift;
    $self->{'display_label'} = shift if @_;


	#This may result in very long dispay_labels
	#if(! defined $self->{'display_label'}){
	#	$self->{'display_label'} = (defined $self->{'desciption'}) ? $self->description()." (".$self->name().")" : $self->name();
	#}

    return $self->{'display_label'};
}
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 (
      $name,
      $dlabel,
	  $desc,
     ) = rearrange([
		    'NAME', 'DISPLAY_LABEL', 'DESCRIPTION',
		   ], @_);
  
  

  throw("Must supply a CellType name\n") if ! $name;

  $self->name($name);
  $self->display_label($dlabel) if $dlabel;
  $self->description($desc) if $desc;

  return $self;
}
General documentation
AUTHORTop
This module was written by Nathan Johnson.
CONTACTTop
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
classTop
  Arg [1]    : (optional) string - class
  Example    : $ft->class('HISTONE');
  Description: Getter and setter of description attribute for FeatureType
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Low Risk