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Bio::EnsEMBL::DensityType Class Reference
Inheritance diagram for Bio::EnsEMBL::DensityType:

List of all members.


Class Summary

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.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Bio::EnsEMBL::Analysis analysis ()
public Int block_size ()
public Int dbID ()
public get_all_DAS_Features ()
public Boolean is_stored ()
public Bio::EnsEMBL::DensityType new ()
public String region_features ()
public Float value_type ()

Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DensityType::analysis ( )
  Arg [1]    : Bio::EnsEMBL::Analysi
  Example    : none
  Description: get/set for attribute analysis
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::DensityType::block_size ( )
  Arg [1]    : int
  Example    : none
  Description: getter/setter for attribute block_size
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
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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:
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Reimplemented from Bio::EnsEMBL::Storable.

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:
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public Float Bio::EnsEMBL::DensityType::value_type ( )
  Arg [1]    : string $value_type
  Example    : none
  Description: gettter/setter for the 
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: