NAME

       Bio::DB::GFF::Aggregator::alignment -- Alignment aggregator

SYNOPSIS

         use Bio::DB::GFF;

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

        -----------------------------
        Aggregator method: alignment
        Main method:       (none)
        Sub methods:       nucleotide_match,EST_match,cDNA_match,expressed_sequence_match,
                           translated_nucleotide_match,protein_match,HSP
        -----------------------------

DESCRIPTION

       Bio::DB::GFF::Aggregator::alignment is one of the default aggregators, and was written to
       be compatible with the C elegans GFF files.  It aggregates raw "similarity" features into
       composite features of type "alignment".  A better name for this class might be
       "gapped_alignment."

       This aggregator does not insist that there be a single top-level feature that spans one
       end of the alignment to the other.  As a result, it can produce truncated alignments if
       the entire alignment is not contained within the segment of interest.

   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

       Because of the large number of similarity features, the aggregate() method is overridden
       in order to perform some optimizations.

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

   part_names
        Title   : part_names
        Usage   : $aggregator->part_names
        Function: return the methods for the sub-parts
        Returns : the full list of aggregated methods
        Args    : none
        Status  : Public