RepeatFeature.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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
 
     http://www.apache.org/licenses/LICENSE-2.0
 
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
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=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/;
 
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