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