Provided by: libbio-perl-perl_1.7.2-2_all bug


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


         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


       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

        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.

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

        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


       None reported.


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


       Lincoln Stein <>.

       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.