Raw content of Bio::EnsEMBL::Funcgen::FeatureType
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::FeatureType
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::FeatureType - A module to represent a FeatureType. i.e. the target of an experiment.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::FeatureType;
=head1 DESCRIPTION
This is a simple class to represent information about a FeatureType, containing the name i.e Brno nomenclature or other controlled/validated name relevant to the class (HISTONE, PROMOTER etc), and description. This module is part of the Ensembl project: /
=head1 AUTHOR
This module was written by Nathan Johnson.
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
#To do
# add coding_transcript/gene methods. Store as xrefs or custom feature_type_coding table? (miRanda etc)
#
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::FeatureType;
use Bio::EnsEMBL::Utils::Argument qw( rearrange ) ;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::Storable;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [-name]: string - name of FeatureType
Arg [-class]: string - class of FeatureType
Arg [-description]: string - descriptiom of FeatureType
Example : my $ft = Bio::EnsEMBL::Funcgen::FeatureType->new(
-name => "H3K9Me",
-class => "HISTONE",
-description => "Generalised methylation of Histone 3 Lysine 9",
);
Description: Constructor method for FeatureType class
Returntype : Bio::EnsEMBL::Funcgen::FeatureType
Exceptions : Throws if name not defined ? and class
Caller : General
Status : Medium risk
=cut
sub new {
my $caller = shift;
my $obj_class = ref($caller) || $caller;
my $self = $obj_class->SUPER::new(@_);
my (
$name,
$desc,
$class,
) = rearrange([
'NAME', 'DESCRIPTION', 'CLASS',
], @_);
if($name){
$self->name($name);
}else{
throw("Must supply a FeatureType name\n");
}
#add test for class and enum? Validate names against Brno etc?
$self->class($class) if $class;
$self->description($desc) if $desc;
return $self;
}
=head2 name
Arg [1] : string - name
Example : my $name = $ft->name();
Description: Getter and setter of name attribute for FeatureType
objects
Returntype : string
Exceptions : None
Caller : General
Status : Low Risk
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if @_;
return $self->{'name'};
}
=head2 description
Arg [1] : (optional) string - description
Example : my $desc = $ft->description();
Description: Getter and setter of description attribute for FeatureType
objects.
Returntype : string
Exceptions : None
Caller : General
Status : Low Risk
=cut
sub description {
my $self = shift;
$self->{'description'} = shift if @_;
return $self->{'description'};
}
=head2 class
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
=cut
sub class{
my $self = shift;
$self->{'class'} = shift if @_;
return $self->{'class'};
}
1;
]]>