Bio::DB::GFF::Aggregator match
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Summary
Bio::DB::GFF::Aggregator::match -- Match aggregator
Package variables
No package variables defined.
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
methodDescriptionCode
part_namesDescriptionCode
main_nameDescriptionCode
Methods description
methodcode    nextTop
 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
main_namecodeprevnextTop
 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
methoddescriptionprevnextTop
sub method {
 'match'
}
part_namesdescriptionprevnextTop
sub part_names {
  return qw(similarity HSP);
}
main_namedescriptionprevnextTop
sub main_name {
  return 'match';
}
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.