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

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::DensityFeature - A feature representing a density, or precentage coverage etc. in a given region.

SYNOPSIS

  use Bio::EnsEMBL::DensityFeature;

  $feature = Bio::EnsEMBL::DensityFeature->new(
    -seq_region    => $region,
    -start         => 1,
    -end           => 1e6,
    -density_type  => $dt,
    -density_value => 98.5
  );

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

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

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

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

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

scaledvalue

 Title   : scaledvalue
 Usage   : $obj->scaledvalue($newval)
 Function:
 Returns : scalar - object's scaled value
 Args    : newvalue (optional)
 Status  : Stable

url

 Title   : url
 Usage   : $obj->url($newval)
 Function:
 Returns : String containing this object's url
 Args    : newvalue (optional)
 Status  : Stable