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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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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.