Bio::DB::GFF::Aggregator::alignment -- 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'], );
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."
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 list ("similarity") Args : none Status : Public
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.