Bio::EnsEMBL::DensityFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::DensityFeature:

Public Member Functions
public Bio::EnsEMBL::DensityFeature	new ()
public Int	strand ()
public Float	density_value ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::DensityType	density_type ()
public Scalar	scaledvalue ()
public String	url ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

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

Definition at line 29 of file DensityFeature.pm.

Member Function Documentation

analysis()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DensityFeature::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

Code:

density_type()

public Bio::EnsEMBL::DensityType Bio::EnsEMBL::DensityFeature::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

Code:

density_value()

public Float Bio::EnsEMBL::DensityFeature::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

Code:

new()

public Bio::EnsEMBL::DensityFeature Bio::EnsEMBL::DensityFeature::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

Code:

scaledvalue()

public Scalar Bio::EnsEMBL::DensityFeature::scaledvalue

(

)

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

Code:

strand()

public Int Bio::EnsEMBL::DensityFeature::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

Code:

url()

public String Bio::EnsEMBL::DensityFeature::url

(

)

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

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/DensityFeature.pm