LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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NAME
Bio::EnsEMBL::DensityFeature - A feature representing a density, or precentage coverage etc. in a given region.
SYNOPSIS
$feature = Bio::EnsEMBL::DensityFeature->new(
-seq_region => $region,
-start => 1,
-end => 1e6,
-density_type => $dt,
-density_value => 98.5
);
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DESCRIPTION
A density feature represents a count, density, or percentage coverage, etc. for a given region.
This module is part of the Ensembl project http://www.ensembl.org
METHODS
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
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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
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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
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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
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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
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scaledvalue
Title : scaledvalue
Usage : $obj->scaledvalue($newval)
Function:
Returns : scalar - object's scaled value
Args : newvalue (optional)
Status : Stable
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url
Title : url
Usage : $obj->url($newval)
Function:
Returns : String containing this object's url
Args : newvalue (optional)
Status : Stable
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