diff variant_effect_predictor/Bio/EnsEMBL/RepeatConsensus.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/RepeatConsensus.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,256 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+package Bio::EnsEMBL::RepeatConsensus;
+
+use strict;
+
+use Bio::EnsEMBL::Storable;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Scalar::Util qw(weaken isweak);
+
+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;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  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.
+
+=head1 AUTHOR
+
+James Gilbert B<email> [e-mail]
+