Bio::DB::GFF::Aggregator::alignment(3) Alignment aggregator


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,


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.


 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.


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


 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