Bio::EnsEMBL::DensityType Class Reference

Inheritance diagram for Bio::EnsEMBL::DensityType:

Public Member Functions
public Bio::EnsEMBL::DensityType	new ()
public Bio::EnsEMBL::Analysis	analysis ()
public Float	value_type ()
public Int	block_size ()
public String	region_features ()
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::DensityType;
 
$type = Bio::EnsEMBL::DensityType->new(
  -analysis   => $analysis,
  -blocksize  => 1000000,
  -value_type => $type
);

Description

A density type represents a density, or percentage coverage etc. in a
given region.

Definition at line 24 of file DensityType.pm.

Member Function Documentation

analysis()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DensityType::analysis

(

)

  Arg [1]    : Bio::EnsEMBL::Analysis
  Description: get/set for attribute analysis
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

block_size()

public Int Bio::EnsEMBL::DensityType::block_size

(

)

  Arg [1]    : int
  Description: getter/setter for attribute block_size
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::DensityType Bio::EnsEMBL::DensityType::new

(

)

  Arg [..]   :  Takes a set of named arguments
  Example    :

$dt = new Bio::EnsEMBL::DensityType::DensityType(
               -analysis  =>  $analysis,
               -blocksize =>  1e6,
               -value_type => 'sum')

  Description: Creates a new Density Type object
  Returntype : Bio::EnsEMBL::DensityType
  Exceptions : blocksize > 0, 
               valuetype must be 'sum' or 'ratio',
               valid analysis object must be passed
  Caller     : general
  Status     : Stable

Code:

region_features()

public String Bio::EnsEMBL::DensityType::region_features

(

)

  Arg [1]    : int $region_features
  Example    :

The number of features per seq_region inside this density_type..

  Description: get/set for attribute region_features
  Returntype : string
  Exceptions : none
  Caller     : general

Code:

value_type()

public Float Bio::EnsEMBL::DensityType::value_type

(

)

  Arg [1]    : string $value_type
  Description: gettter/setter for the type 
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

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