Bio::DB::GFF::Homol - A segment of DNA that is homologous to another

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

Top

Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another

SYNOPSIS

Top

See Bio::DB::GFF.

DESCRIPTION

Top

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->target() method.

METHODS

Top

name

 Title   : name
 Usage   : $name = $homol->name
 Function: get the ID of the homology object
 Returns : a string
 Args    : none
 Status  : Public

asString

 Title   : asString
 Usage   : $name = $homol->asString
 Function: same as name(), for operator overloading
 Returns : a string
 Args    : none
 Status  : Public

id

 Title   : id
 Usage   : $id = $homol->id
 Function: get database ID in class:id format
 Returns : a string
 Args    : none
 Status  : Public

BUGS

Top

This module is still under development.

SEE ALSO

Top

bioperl, Bio::DB::GFF, Bio::DB::RelSegment

AUTHOR

Top

Lincoln Stein <lstein@cshl.org>.

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.

BioPerl documentation Contained in the BioPerl distribution. 
package Bio::DB::GFF::Homol;
use strict;

use base qw(Bio::DB::GFF::Segment);


sub name     { shift->refseq }


sub asString { shift->name }



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__;
}


1;