Raw content of Bio::EnsEMBL::SimpleFeature
<![CDATA[=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::SimpleFeature - A simple feature with a location and label
=head1 SYNOPSIS
use Bio::EnsEMBL::SimpleFeature;
$feature = Bio::EnsEMBL::SimpleFeature->new(
-start => 100,
-end => 220,
-strand => -1,
-slice => $slice,
-analysis => $analysis,
-score => 58,
-display_label => 'EponineTSS',
-dbID => 1230,
-adaptor => $adaptor
);
=head1 DESCRIPTION
This is a simple feature which extends the Feature class to add
display_label and score attributes.
=head1 METHODS
=cut
use strict;
package Bio::EnsEMBL::SimpleFeature;
use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [DISPLAY_LABEL]: The label assigned to this simple feature
Arg [...] : Named arguments passed to superclass
Example : $feature = Bio::EnsEMBL::SimpleFeature->new
(-start => 1,
-end => 100,
-strand => 1,
-slice => $slice,
-analysis => $analysis,
-adaptor => $adaptor,
-dbID => 10,
-display_label => 'EponineTSS',
-score => 100);
Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
of this method are instantiated, rather than this class itself.
Returntype : Bio::EnsEMBL::Feature
Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
Caller : general, subclass constructors
Status : Stable
=cut
sub new {
my $caller = shift;
#allow this to be called as class or object method
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($display_label, $score) = rearrange(['DISPLAY_LABEL','SCORE'],@_);
$self->{'display_label'} = $display_label;
$self->{'score'} = $score;
return $self;
}
=head2 new_fast
Arg [1] : hashref to be blessed
Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
Exceptions : none
Returntype : Bio::EnsEMBL::Feature
Caller : general, subclass constructors
Status : Stable
=cut
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
=head2 display_label
Arg [1] : (optional) string $value
Example : $label = $simple_feature->display_label();
Description: Getter/Setter for the display label associated with this
feature.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub display_label{
my $self = shift;
$self->{'display_label'} = shift if(@_);
return $self->{'display_label'};
}
=head2 display_id
Arg [1] : none
Example : print $rf->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For simple features this is the
display_label if it is available otherwise it is an empty
string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_id {
my $self = shift;
return $self->{'display_label'} || '';
}
=head2 score
Arg [1] : (optional) string $value
Example : $score = $simple_feature->score();
Description: Getter/Setter for the score associated with this
feature.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub score {
my $self = shift;
$self->{'score'} = shift if(@_);
return $self->{'score'};
}
1;
]]>