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Manual Reference Pages  -  BIO::DB::GFF::AGGREGATOR::ALIGNMENT (3)

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NAME

Bio::DB::GFF::Aggregator::alignment -- Alignment aggregator

CONTENTS

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.

    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



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perl v5.20.3 BIO::DB::GFF::AGGREGATOR::ALIGNMENT (3) 2016-04-05

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