Bio::DB::GFF::Aggregator match
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Summary
Bio::DB::GFF::Aggregator::match -- Match aggregator
Package variables
No package variables defined.
Included modules
Bio::DB::GFF::Aggregator
Inherit
Bio::DB::GFF::Aggregator
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
main_nameDescriptionCode
methodDescriptionCode
part_namesDescriptionCode
Methods description
main_namecode    nextTop
 Title   : main_name
 Usage   : $aggregator->main_name
 Function: return the method for the main component
 Returns : the string "match"
 Args    : none
 Status  : Public
methodcodeprevnextTop
 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "match"
 Args    : none
 Status  : Public
part_namescodeprevnextTop
 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list "similarity", "HSP"
 Args    : none
 Status  : Public
Methods code
main_namedescriptionprevnextTop
sub main_name {
  return 'match';
}
methoddescriptionprevnextTop
sub method {
 'match'
}
part_namesdescriptionprevnextTop
sub part_names {
  return qw(similarity HSP);
}
General documentation
BUGSTop
None reported.
SEE ALSOTop
Bio::DB::GFF, Bio::DB::GFF::Aggregator
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.