RepeatConsensus.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
 
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=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 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.