Bio::DB::GFF::Aggregator::alignment.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::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
  -----------------------------
 
 

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