Raw content of Bio::EnsEMBL::RepeatFeature
<![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
=head1 NAME
Bio::EnsEMBL::RepeatFeature - A feature representing a repeat on a piece of
sequence.
=head1 SYNOPSIS
my $rf = new Bio::EnsEMBL::Feature(
-start => 100,
-end => 220,
-strand => -1,
-slice => $slice,
-analysis => $analysis,
-repeat_consensus => $rc,
-hstart => 10,
-hend => 100,
-hstrand => 1,
-score => 83.2
);
my $hstart = $feat->hstart;
my $hend = $feat->hend;
# move the feature to the chromosomal coordinate system
$feature = $feature->transform('chromosome');
# move the feature to a different slice
# (possibly on another coord system)
$feature = $feature->transfer($new_slice);
# project the feature onto another coordinate system possibly across
# boundaries:
@projection = @{ $feature->project('contig') };
# change the start, end, and strand of the feature in place
$feature->move( $new_start, $new_end, $new_strand );
=head1 DESCRIPTION
This a feature representing a repeat region on a sequence
=head1 METHODS
=cut
package Bio::EnsEMBL::RepeatFeature;
use strict;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars '@ISA';
@ISA = qw{ Bio::EnsEMBL::Feature };
=head2 new_fast
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used. It is only used by
RepeatFeatureAdaptors (when thousands of repeats need to be
quickly created). The constructor 'new' should be used in
most instances.
Returntype : Bio::EnsEMBL::RepeatFeature
Exceptions : none
Caller : RepeatFeatureAdaptors
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless $hashref, $class;
}
=head2 new
Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
The repeat consensus for this repeat feature
Arg [HSTART] : int (optional)
The hit start on the consensus sequence
Arg [HEND] : int (optional)
The hit end on the consensus sequence
Arg [SCORE] : float (optional)
The score
Arg [...] : Named arguments to superclass constructor
(see Bio::EnsEMBL::Feaure)
Example : $rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
-HSTART => 10,
-HEND => 100,
-SCORE => 58.0,
-START => 1_000_100,
-END => 1_000_190,
-STRAND => 1,
-ANALYSIS => $an,
-SLICE => $chr_slice);
Description: Creates a new Bio::EnsEMBL::RepeatFeature object
Returntype : Bio::EnsEMBL::RepeatFeature
Exceptions : none
Caller : RepeatFeatureAdaptors
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($repeat_consensus, $hstart, $hend, $score) =
rearrange(['REPEAT_CONSENSUS','HSTART','HEND','SCORE'], @_);
$self->repeat_consensus($repeat_consensus);
$self->{'hstart'} = $hstart;
$self->{'hend'} = $hend;
$self->{'score'} = $score;
return $self;
}
=head2 repeat_consensus
Arg [1] : (optional) Bio::EnsEMBL::RepeatConsensus
Example : $repeat_consensus = $repeat->repeat_consensus;
Description: Getter/Setter for the repeat consensus of this repeat
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
Status : Stable
=cut
sub repeat_consensus {
my $self = shift;
if(@_) {
my $rc = shift;
if(defined($rc)) {
if(!ref($rc) || !$rc->isa('Bio::EnsEMBL::RepeatConsensus')) {
throw('RepeatConsensus arg must be a Bio::EnsEMBL::RepeatConsensus');
}
}
$self->{'repeat_consensus'} = $rc;
}
return $self->{'repeat_consensus'};
}
=head2 hstart
Arg [1] : (optional) int $hstart
Example : $hit_start = $repeat->hstart;
Description: Getter/Setter for the start bp of this repeat match on the
consensus sequence.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub hstart {
my $self = shift;
$self->{'hstart'} = shift if(@_);
return $self->{'hstart'};
}
=head2 score
Arg [1] : (optional) float $score
Example : $score = $repeat->score();
Description: Getter/Setter for the score of this repeat feature
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub score {
my $self = shift;
$self->{'score'} = shift if(@_);
return $self->{'score'};
}
=head2 hend
Arg [1] : (optional) int $hend
Example : $hit_end = $repeat->hend;
Description: Getter/Setter for the end bp of this repeat match on the
consensus sequence.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub hend {
my $self = shift;
$self->{'hend'} = shift if(@_);
return $self->{'hend'};
}
=head2 hstrand
Arg [1] : none
Example : none
Description: always returns 1. method exists for consistancy with other
features.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub hstrand {
return 1;
}
=head2 display_id
Arg [1] : none
Example : print $rf->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For repeat_features this is the
name of the repeat consensus if it is available otherwise it is
an empty string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_id {
my $self = shift;
my $id = '';
my $rc = $self->{'repeat_consensus'};
if($rc) {
$id = $rc->name();
}
return $id;
}
1;
__END__
=head1 NAME - Bio::EnsEMBL::RepeatFeature
=head1 AUTHOR
James Gilbert B<email> jgrg@sanger.ac.uk
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