Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.


# get a Bio::SeqFeature::CollectionI somehow # perhaps a Bio::SeqFeature::Collection
     use Bio::SeqFeature::Collection;
     my $collection = Bio::SeqFeature::Collection->new();
     $collection->features(-attributes => 
                           [ { 'location' => Bio::Location::Simple->new
                                   (-start=> 1, -end => 300) ,
                                   'overlaps' }]);


This interface describes the basic methods needed for a collection of Sequence Features.


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AUTHOR - Jason Stajich



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  Title   : add_features
  Usage   : $collection->add_features(\@features);
  Returns : number of features added
  Args    : arrayref of Bio::SeqFeatureI objects to index


  Title   : features
  Usage   : my @f = $collection->features(@args);
  Returns : a list of Bio::SeqFeatureI objects
  Args    : see below
  Status  : public

This routine will retrieve features associated with this collection object. It can be used to return all features, or a subset based on their type, location, or attributes.

   -types     List of feature types to return.  Argument is an array
              of Bio::Das::FeatureTypeI objects or a set of strings
              that can be converted into FeatureTypeI objects.
   -callback   A callback to invoke on each feature.  The subroutine
               will be passed to each Bio::SeqFeatureI object in turn.
   -attributes A hash reference containing attributes to match.

The -attributes argument is a hashref containing one or more attributes to match against:

   -attributes => { Gene => 'abc-1',
                    Note => 'confirmed' }

Attribute matching is simple exact string matching, and multiple attributes are ANDed together. See Bio::DB::ConstraintsI for a more sophisticated take on this.

If one provides a callback, it will be invoked on each feature in turn. If the callback returns a false value, iteration will be interrupted. When a callback is provided, the method returns undef.