Raw content of Bio::EnsEMBL::RepeatFeature =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