Raw content of Bio::DB::GFF::Aggregator::alignment =head1 NAME Bio::DB::GFF::Aggregator::alignment -- Alignment aggregator =head1 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: similarity, HSP ----------------------------- =head1 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. =cut package Bio::DB::GFF::Aggregator::alignment; use strict; use Bio::DB::GFF::Aggregator; use vars qw(@ISA); @ISA = qw(Bio::DB::GFF::Aggregator); =head2 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. =cut # we look for features of type Sequence and add them to a pseudotype transcript sub aggregate { my $self = shift; my $features = shift; my $factory = shift; my $matchsub = $self->match_sub($factory) or return; my $passthru = $self->passthru_sub($factory); my $method = $self->get_method; my (%alignments,%targets,@result); warn "running alignment aggregator" if $factory->debug; for my $feature (@$features) { if ($matchsub->($feature)) { my $group = $feature->{group}; my $source = $feature->source; unless (exists $alignments{$group,$source}) { my $type = Bio::DB::GFF::Typename->new($method,$source); my $f = $feature->clone; # this is a violation of OO encapsulation, but need to do it this way # to achieve desired performance @{$f}{qw(type score phase)} = ($type,undef,undef); $alignments{$group,$source} = $f or next; } my $main = $alignments{$group,$source}; $main->add_subfeature($feature); push @result,$feature if $passthru && $passthru->($feature); } else { push @result,$feature; } } warn "running aligner adjuster" if $factory->debug; for my $alignment (values %alignments) { $alignment->adjust_bounds; $alignment->compound(1); push @result,$alignment; } warn "aligner done" if $factory->debug; @$features = @result; } =head2 method Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "alignment" Args : none Status : Public =cut sub method { 'alignment' } =head2 part_names Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list ("similarity","HSP") Args : none Status : Public =cut sub part_names { my $self = shift; return qw(similarity HSP); } 1;