Bio::DB::GFF::Aggregator alignment
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Summary
Bio::DB::GFF::Aggregator::alignment -- Alignment aggregator
Package variables
No package variables defined.
Inherit
Bio::DB::GFF::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.
Methods
aggregateDescriptionCode
methodDescriptionCode
part_namesDescriptionCode
Methods description
aggregatecode    nextTop
 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 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.
methodcodeprevnextTop
 Title   : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "alignment"
Args : none
Status : Public
part_namescodeprevnextTop
 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
Methods code
aggregatedescriptionprevnextTop
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;
}
methoddescriptionprevnextTop
sub method {
 'alignment'
}
part_namesdescriptionprevnextTop
sub part_names {
  my $self = shift;
 return qw(nucleotide_match EST_match cDNA_match
	   expressed_sequence_match
	   translated_nucleotide_match
	   protein_match HSP);
}

1;
}
General documentation
No general documentation available.