NAME

       Bio::DB::GFF::Aggregator::waba_alignment -- A WABA alignment

SYNOPSIS

         use Bio::DB::GFF;

         # Open the sequence database
         my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                          -dsn     => 'dbi:mysql:elegans42',
                                          -aggregator => ['waba_alignment'],
                                        );
         # fetch the synthetic feature type "waba_alignment"
         my @waba    = $db->features('waba_alignment');

        -------------------------------------------------------------------------------------
        Aggregator method: waba_alignment
        Main method:       -none
        Sub methods:       nucleotide_match:waba_weak nucleotide_match:waba_strong
                           nucleotide_match::waba_coding
        -------------------------------------------------------------------------------------

DESCRIPTION

       Bio::DB::GFF::Aggregator::waba_alignment handles the type of alignments produced by Jim
       Kent's WABA program, and was written to be compatible with the C elegans GFF files.  It
       aggregates the following feature types into an aggregate type of "waba_alignment":

          nucleotide_match:waba_weak
          nucleotide_match:waba_strong
          nucleotide_match:waba_coding

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

   part_names
        Title   : part_names
        Usage   : $aggregator->part_names
        Function: return the methods for the sub-parts
        Returns : the list "nucleotide_match:waba_weak", "nucleotide_match:waba_strong" and "nucleotide_match:waba_coding"
        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.

perl v5.18.1                                2013-10-Bio::DB::GFF::Aggregator::waba_alignment(3pm)