Bio::DB::GFF::Aggregator::match.3pm

Langue: en

Autres versions - même langue

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

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.