Bio::DB::GFF Homol
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Summary
Bio::DB::GFF::Homol -- A segment of DNA that is homologous to another
Package variables
No package variables defined.
Included modules
Bio::DB::GFF::Segment
Inherit
Bio::DB::GFF::Segment
Synopsis
See Bio::DB::GFF.
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->target() method.
Methods
asStringDescriptionCode
idDescriptionCode
nameDescriptionCode
new_from_segment
No description
Code
Methods description
asStringcode    nextTop
 Title   : asString
 Usage   : $name = $homol->asString
 Function: same as name(), for operator overloading
 Returns : a string
 Args    : none
 Status  : Public
idcodeprevnextTop
 Title   : id
 Usage   : $id = $homol->id
 Function: get database ID in class:id format
 Returns : a string
 Args    : none
 Status  : Public
namecodeprevnextTop
 Title   : name
 Usage   : $name = $homol->name
 Function: get the ID of the homology object
 Returns : a string
 Args    : none
 Status  : Public
Methods code
asStringdescriptionprevnextTop
sub asString {
 shift->name
}
iddescriptionprevnextTop
sub id {
  my $self = shift;
  return "$self->{class}:$self->{name}";
}
namedescriptionprevnextTop
sub name {
 shift->refseq
}
new_from_segmentdescriptionprevnextTop
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__;
}
General documentation
BUGSTop
This module is still under development.
SEE ALSOTop
bioperl, Bio::DB::GFF, Bio::DB::RelSegment
AUTHORTop
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.