Bio::DB::GFF::AggregatUseraContributed PBio::DB::GFF::Aggregator::alignment(3)NAMEBio::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
-----------------------------
DESCRIPTIONBio::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
perl v5.14.12011-0Bio::DB::GFF::Aggregator::alignment(3)
