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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;
$Bio::DB::GFF::Homol::VERSION = '1.7.4';
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;
|
