Raw content of Bio::EnsEMBL::RepeatConsensus
<![CDATA[=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
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