view variant_effect_predictor/Bio/EnsEMBL/RepeatFeature.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=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

=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::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);

use base qw/Bio::EnsEMBL::Feature/;

=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> [e-mail]