Provided by: libbio-perl-perl_1.7.6-3_all bug


       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.