Raw content of Bio::EnsEMBL::DensityFeature
<![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::DensityFeature - A feature representing a density, or
precentage coverage etc. in a given region.
=head1 SYNOPSIS
use Bio::EnsEMBL::DensityFeature;
$feature = Bio::EnsEMBL::DensityFeature->new(
-seq_region => $region,
-start => 1,
-end => 1e6,
-density_type => $dt,
-density_value => 98.5
);
=head1 DESCRIPTION
A density feature represents a count, density, or percentage coverage,
etc. for a given region.
This module is part of the Ensembl project
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::DensityFeature;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::DensityType;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [SEQ_REGION] : the sequence over which the density was calculated.
Arg [START] : start point on the seq at which density was calulated.
Arg [END] : end point on the seq at which density was calulated.
Arg [DENSITY_TYPE] : the type of density calculated.
Arg [DENSITY_VALUE] : the density.
Arg [...] : Named arguments passed to superclass
Example : $feature = Bio::EnsEMBL::DensityFeature->new
(-seq_region => $region,
-start => 1,
-end => 1e6,
-density_type => $dt,
-density_value => 98.5)
Description: Creates a new density feature.
Returntype : Bio::EnsEMBL::DensityFeature
Exceptions : throw if invalid density value type is provided
Caller : general
Status : Stable
=cut
sub new {
my $caller = shift;
#allow constructor to be called as class or object method
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my($seq_region, $start, $end, $dt, $dv) =
rearrange(['SEQ_REGION', 'START', 'END', 'DENSITY_TYPE', 'DENSITY_VALUE'],
@_);
throw("Density value must be >= 0.") if($dv < 0);
if(!defined($dt)){
throw("Density Type is NOT optional.");
}
$self->{'density_type'} = $dt;
$self->{'density_value'} = $dv;
$self->{'slice'} = $seq_region;
$self->{'start'} = $start;
$self->{'end'} = $end;
return $self;
}
=head2 new_fast
Arg [...] : none
Example : $feature = Bio::EnsEMBL::DensityFeature->new_fast();
Description: Creates a new density feature.
Returntype : Bio::EnsEMBL::DensityFeature
Exceptions : none
Caller : general
Status : Stable
=cut
sub new_fast{
my $caller = shift;
#allow constructor to be called as class or object method
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
return $self;
}
=head2 strand
Arg [1] : none
Example : $strand = $df->strand();
Description: Getter fot the strand attribute. Density features always have
strand 0 and this attribute is not settable.
Returntype : int (always 0)
Exceptions : warning if an attempt is made to set the strand
Caller : general
Status : Stable
=cut
sub strand {
my $self = shift;
warning("DensityFeature strand is not settable") if(@_);
return 0;
}
=head2 density_value
Arg [1] : (optional) float $density_value
Example : $dv = $density_feature->density_value();
Description: Getter/Setter for the density value of this DensityFeature.
The density value may be a count, a percentage, or a coverage
of a feature type in the area defined by this feature.
Returntype : float
Exceptions : throw if a negative density value is provided
Caller : general
Status : Stable
=cut
sub density_value {
my $self = shift;
if(@_) {
my $density_value = shift;
throw("Density value must be >= 0.") if($density_value < 0);
$self->{'density_value'} = $density_value;
}
return $self->{'density_value'};
}
=head2 analysis
Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis
New value for the analysis of the attached DensityType
Example : print $df->analysis()->logic_name();
Description: Overridden superclass analysis method, to chain to analysis
method on attached DensityType.
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
Status : Stable
=cut
sub analysis {
my $self = shift;
my $dt = $self->density_type();
return undef if(!$dt);
return $dt->analysis(@_);
}
=head2 density_type
Arg [1] : string $newval (optional)
The new value to set the density_value_type attribute to
Example : $density_value_type = $obj->density_value_type()
Description: Getter/Setter for the density_value_type attribute
Returntype : Bio::EnsEMBL::DensityType
Exceptions : if object passed is not of type DensityType
Caller : general
Status : Stable
=cut
sub density_type{
my $self = shift;
if(@_) {
my $type = shift;
if( !ref $type || !$type->isa("Bio::EnsEMBL::DensityType")){
throw("object passed must be an ensembl DensityType ".
"not a [".ref($type)."]");
}
else{
$self->{'density_type'}=$type;
}
}
return $self->{'density_type'};
}
###BG########
=head2 scaledvalue
Title : scaledvalue
Usage : $obj->scaledvalue($newval)
Function:
Returns : this objects scaled value
Args : newvalue (optional)
Status : Stable
=cut
sub scaledvalue{
my $obj = shift;
if( @_ ) {
my $scaledvalue = shift;
$obj->{'scaledvalue'} = $scaledvalue;
}
return $obj->{'scaledvalue'};
}
=head2 url
Title : url
Usage : $obj->url($newval)
Function:
Returns : this object's url
Args : newvalue (optional)
Status : Stable
=cut
sub url{
my $obj = shift;
if( @_ ) {
my $url = shift;
$obj->{'url'} = $url;
}
return $obj->{'url'};
}
1;
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