=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=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
$Bio::EnsEMBL::RepeatFeature::VERSION = '112.0_55'; # TRIAL
$Bio::EnsEMBL::RepeatFeature::VERSION = '112.055';
use strict;
use constant SEQUENCE_ONTOLOGY => {
acc => 'SO:0000657',
term => 'repeat_region',
};
=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;
}
=head2 summary_as_hash
Example : $repeat_feature_summary = $protein_feature->summary_as_hash();
Description : Retrieves a textual summary of this Repeat feature.
Not inherited from Feature.
Returns : hashref of arrays of descriptive strings
Status : Intended for internal use
=cut
sub summary_as_hash {
my $self = shift;
my %summary;
$summary{'start'} = $self->seq_region_start;
$summary{'end'} = $self->seq_region_end;
$summary{'strand'} = $self->strand;
$summary{'seq_region_name'} = $self->seq_region_name;
$summary{'description'} = $self->display_id;
$summary{'assembly_name'} = $self->slice->coord_system->version();
return \%summary;
}
1;
__END__
=head1 NAME - Bio::EnsEMBL::RepeatFeature