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LRR / Polloc-v1.5.3 / lib / Bio / Polloc / Locus / extend.pm 

            

              
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=head1 NAME
Bio::Polloc::Locus::extend - A feature based on another one
=head1 DESCRIPTION
A feature of a sequence, inferred by similarity or surrounding
regions similar to those of a known feature.  Implements
L<Bio::Polloc::LocusI>.
=head1 AUTHOR - Luis M. Rodriguez-R
Email lmrodriguezr at gmail dot com
=cut
package Bio::Polloc::Locus::extend;
use base qw(Bio::Polloc::LocusI);
use strict;
our $VERSION = 1.0503; # [a-version] from Bio::Polloc::Polloc::Version
=head1 APPENDIX
Methods provided by the package
=head2 new
Creates a B<Bio::Polloc::Locus::repeat> object.
=head3 Arguments
=over
=item -basefeature I<Bio::Polloc::LocusI object>
The reference feature or part of the reference collection.
=item -score I<float>
The score of extension (bit-score on BLAST or score on HMMer, for example).
=back
=cut
sub new {
   my($caller,@args) = @_;
   my $self = $caller->SUPER::new(@args);
   $self->_initialize(@args);
   return $self;
}
=head2 basefeature
Gets/sets the reference feature of the extension.  Be careful, this can also
refer to one feature in a collection of reference.  Avoid using specific data
from this feature.
=head3 Arguments
The reference feature (L<Bio::Polloc::LocusI> object, optional).
=head3 Returns
The reference feature (L<Bio::Polloc::LocusI> object or undef).
=cut
sub basefeature {
   my($self,$value) = @_;
   if (defined $value){
      $self->{'_basefeature'} = $value;
      $self->family($value->family);
   }
   return $self->{'_basefeature'};
}
=head2 score
Gets/sets the score.
=head3 Arguments
The score (float, optional).
=head3 Returns
The score (float or undef).
=cut
sub score {
   my($self,$value) = @_;
   $self->{'_score'} = $value+0 if defined $value;
   return $self->{'_score'};
}
=head2 distance
Tries to calculate the distance using the base-feature's C<distance()>
method.  See L<Bio::Polloc::LocusI->distance()>.
=head3 Throws
L<Bio::Polloc::Polloc::Error>.
=cut
sub distance {
   my ($self, @args) = @_;
   $self->throw('Impossible to find a base feature.') unless defined $self->basefeature;
   return $self->basefeature->distance(-locusref=>$self, @args);
}
=head1 INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*
=head2 _initialize
=cut
sub _initialize {
   my($self,@args) = @_;
   my($basefeature,$score) = $self->_rearrange([qw(BASEFEATURE SCORE)], @args);
   $self->type('extend');
   $self->comments("Extended feature");
   $self->basefeature($basefeature);
   $self->score($score);
}
1;