SENDU / bioperl-1.5.2_005-RC / Bio / DB / GFF / Homol.pm 

            

              
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=head1 NAME
Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another
=head1 SYNOPSIS
See L<Bio::DB::GFF>.
=head1 DESCRIPTION
Bio::DB::GFF::Homol is a named subtype of Bio::DB::GFF::Segment.  It
inherits all the methods of its parent, and was created primarily to
allow for isa() queries and for compatibility with
Ace::Sequence::Homol.  
A Homol object is typically returned as the method result of the
Bio::DB::GFF::Feature-E<gt>target() method.
=head1 METHODS
=cut
package Bio::DB::GFF::Homol;
use strict;
use base qw(Bio::DB::GFF::Segment);
=head2 name
 Title   : name
 Usage   : $name = $homol->name
 Function: get the ID of the homology object
 Returns : a string
 Args    : none
 Status  : Public
=cut
sub name     { shift->refseq }
=head2 asString
 Title   : asString
 Usage   : $name = $homol->asString
 Function: same as name(), for operator overloading
 Returns : a string
 Args    : none
 Status  : Public
=cut
sub asString { shift->name }
=head2 id
 Title   : id
 Usage   : $id = $homol->id
 Function: get database ID in class:id format
 Returns : a string
 Args    : none
 Status  : Public
=cut
sub id       {
  my $self = shift;
  return "$self->{class}:$self->{name}";
}
sub new_from_segment {
  my $package   = shift;
  $package      = ref $package if ref $package;
  my $segment   = shift;
  my $new = {};
  @{$new}{qw(factory sourceseq start stop strand class ref refstart refstrand)}
    = @{$segment}{qw(factory sourceseq start stop strand class ref refstart refstrand)};
  return bless $new,__PACKAGE__;
}
=head1 BUGS
This module is still under development.
=head1 SEE ALSO
L<bioperl>, L<Bio::DB::GFF>, L<Bio::DB::RelSegment>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
1;