Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::DB::GFF::Aggregator::clone -- Clone aggregator

SYNOPSIS

         use Bio::DB::GFF;

         # Open the sequence database
         my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                          -dsn     => 'dbi:mysql:elegans42',
                                          -aggregator => ['transcript','clone'],
                                        );

        ----------------------------------------------------------------------------
        Aggregator method: clone
        Main method:       -none-
        Sub methods:       Clone_left_end Clone_right_end region:Genomic_canonical
        ----------------------------------------------------------------------------

DESCRIPTION

       Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and was written to be
       compatible with the C elegans GFF files.  It aggregates raw "Clone_left_end",
       "Clone_right_end", and "region:Genomic_canonical" features into composite features of type
       "clone".

   aggregate
        Title   : aggregate
        Usage   : $features = $a->aggregate($features,$factory)
        Function: aggregate a feature list into composite features
        Returns : an array reference containing modified features
        Args    : see L<Bio::DB::GFF::Aggregator>
        Status  : Public

       The WormBase GFF model is unusual in that clones aren't identified as a single feature
       with start and stop positions, but as two features, a "left end" and a "right end".  One
       or both of these features may be absent.  In order to accommodate this, the aggregator
       will return undef for the start and/or stop if one or both of the ends are missing.

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

   part_names
        Title   : part_names
        Usage   : $aggregator->part_names
        Function: return the methods for the sub-parts
        Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
        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.