Bio::EnsEMBL::RepeatConsensus Class Reference

Inheritance diagram for Bio::EnsEMBL::RepeatConsensus:

Public Member Functions
public Bio::EnsEMBL::RepeatConsensus	new ()
public String	name ()
public Int	length ()
public String	repeat_class ()
public String	repeat_type ()
public String	desc ()
public String	repeat_consensus ()
public String	seq ()
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

Definition at line 5 of file RepeatConsensus.pm.

Member Function Documentation

desc()

public String Bio::EnsEMBL::RepeatConsensus::desc

(

)

  Arg [1]    : none
  Example    :

$desc = $repeat_consensus->desc()

  Description: Getter for the description of this repeat consensus as extracted
               from the repeat_class.  This method is probably useless.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Medium risk

Code:

length()

public Int Bio::EnsEMBL::RepeatConsensus::length

(

)

  Arg [1]    : int $length (optional)
  Example    :

$length = $repeat_consensus->length()

  Description: Getter/Setter for the length of this repeat_consensus
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

name()

public String Bio::EnsEMBL::RepeatConsensus::name

(

)

  Arg [1]    : string $name (optional)
  Example    :

$name = $repeat_consensus->name()

  Description: Getter/Setter for the name of this repeat_consensus
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::RepeatConsensus::new

(

)

  Arg [NAME] : string (optional)
               The name of this repeat consensus
  Arg [LENGTH]: int (optional)
               The length of the repeat consensus sequence
  Arg [REPEAT_CLASS]: string (optional)
               The type of repeat consensus
  Arg [REPEAT_CONSENSUS]: string (optional)
               The sequence of this repeat consensus
  Arg [REPEAT_TYPE]: string 
               Its like class only more general
  Arg [...]: Named arguments to superclass constructor
             (see Bio::EnsEMBL::Storable)
  Example    :

$rc = Bio::EnsEMBL::RepeatConsensus->new
                      (-REPEAT_CONSENSUS => 'AATG'
                       -NAME => '(AATG)n',
                       -REPEAT_CLASS => 'Simple_repeat',
                       -LENGTH => '4',
                       -DBID => 1023,
                       -ADAPTOR => $rc_adaptor);

  Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : RepeatFeatureAdaptors
  Status     : Stable

Code:

repeat_class()

public String Bio::EnsEMBL::RepeatConsensus::repeat_class

(

)

  Arg [1]    : string $class (optional)
               The class of 
  Example    :

$class = $repeat_consensus->repeat_class()

  Description: Getter/Setter for the class of this repeat_consensus
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

repeat_consensus()

public String Bio::EnsEMBL::RepeatConsensus::repeat_consensus

(

)

  Arg [1]    : string $consensus_seq (optional)
               The sequence of this repeat consensus
  Example    :

$consensus = $repeat_consensus->repeat_consensus();

  Description: Getter/Setter for the sequence of this repeat_consensus.
  Returntype : string
  Exceptions : none
  Caller     : general

Code:

repeat_type()

public String Bio::EnsEMBL::RepeatConsensus::repeat_type

(

)

  Arg [1]    : string $type (optional)
               The type of the consensus 
  Example    :

$type = $repeat_consensus->repeat_type()

  Description: Getter/Setter for the type of this repeat_consensus
  Returntype : string
  Exceptions : none
  Caller     : general

Code:

seq()

public String Bio::EnsEMBL::RepeatConsensus::seq

(

)

  Arg [1]    : none
  Example    :

none

  Description: Returns the repeat consensus.  This method is useless - Use
               repeat_consensus() instead.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

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