Raw content of Bio::EnsEMBL::RepeatConsensus =head1 LICENSE Copyright (c) 1999-2009 The European Bioinformatics Institute and Genome Research Limited. All rights reserved. This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at <ensembl-dev@ebi.ac.uk>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. =cut package Bio::EnsEMBL::RepeatConsensus; use strict; use Bio::EnsEMBL::Storable; use Bio::EnsEMBL::Utils::Argument qw(rearrange); use vars qw(@ISA); @ISA = qw(Bio::EnsEMBL::Storable); =head2 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 =cut sub new { my $caller = shift; my $class = ref($caller) || $caller; my $self = $class->SUPER::new(@_); my ($name, $length, $repeat_class, $repeat_consensus, $repeat_type ) = rearrange(['NAME', 'LENGTH', 'REPEAT_CLASS', 'REPEAT_CONSENSUS', 'REPEAT_TYPE'], @_); $self->{'name'} = $name; $self->{'length'} = $length; $self->{'repeat_class'} = $repeat_class; $self->{'repeat_consensus'} = $repeat_consensus; $self->{'repeat_type'} = $repeat_type; return $self; } =head2 new_fast Arg [1] : hashref to bless as a new RepeatConsensus Description: Creates a new Bio::EnsEMBL::RepeatConsensus object Returntype : Bio::EnsEMBL::RepeatConsensus Exceptions : none Caller : internal Status : Stable =cut sub new_fast { my $class = shift; my $hashref = shift; return bless $hashref, $class; } =head2 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 =cut sub name { my $self = shift; $self->{'name'} = shift if(@_); return $self->{'name'}; } =head2 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 =cut sub length { my $self = shift; $self->{'length'} = shift if(@_); return $self->{'length'}; } =head2 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 =cut sub repeat_class { my $self = shift; $self->{'repeat_class'} = shift if(@_); return $self->{'repeat_class'}; } =head2 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 =cut sub repeat_type { my $self = shift; $self->{'repeat_type'} = shift if(@_); return $self->{'repeat_type'}; } =head2 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 =cut sub desc { my $self = shift; my $class = $self->repeat_class or return; return "class=$class"; } =head2 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 =cut sub repeat_consensus { my $self = shift; $self->{'repeat_consensus'} = shift if(@_); return $self->{'repeat_consensus'}; } =head2 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 =cut sub seq { my( $self ) = @_; return $self->repeat_consensus; } 1; __END__ =head1 NAME - Bio::EnsEMBL::RepeatConsensus =head1 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. =head1 AUTHOR James Gilbert B<email> jgrg@sanger.ac.uk