NAME

Bio::DB::GFF::Aggregator::match -- Match 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.

method

            

              
              
Title   : method
Usage   : $aggregator->method
Function: return the method for the composite object
Returns : the string "match"
Args    : none
Status  : Public
            
          

part_names

            

              
              
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_name

            

              
              
Title   : main_name
Usage   : $aggregator->main_name
Function: return the method for the main component
Returns : the string "match"
Args    : none
Status  : Public
            
          

BUGS

None reported.

SEE ALSO

Bio::DB::GFF, Bio::DB::GFF::Aggregator

AUTHOR

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.