Bio::DB::GFF::Aggregator
match
Summary
Bio::DB::GFF::Aggregator::match -- Match aggregator
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['match'],
);
-------------------------------------------------
Aggregator method: match
Main method: match
Sub methods: similarity HSP
-------------------------------------------------
Description
This aggregator is used for Sequence Ontology-compatible gapped
alignments, in which there is a single top-level alignment called
"match" and a series of subalignments called either "similarity" or
"HSP".
Also see the "alignment" aggregator.
Methods
Methods description
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "match"
Args : none
Status : Public |
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list "similarity", "HSP"
Args : none
Status : Public |
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "match"
Args : none
Status : Public |
Methods code
sub part_names
{ return qw(similarity HSP); } | sub main_name
{ return 'match'; } | | require_whole_object | description | prev | next | Top |
sub require_whole_object
{1 } | General documentation
None reported.
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.