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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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

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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

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

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

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

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

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

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

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

NAME - Bio::EnsEMBL::RepeatConsensus

DESCRIPTION

This object represents an entry in the repeat_consensus table.

It can contain the consensus sequence for a repeat such as a particular Alu, or "cag" for a simple triplet repeat.