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

NAME

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

SYNOPSIS

       # get a Bio::SeqFeature::CollectionI somehow # perhaps a Bio::SeqFeature::Collection

           use Bio::SeqFeature::Collection;
           my $collection = Bio::SeqFeature::Collection->new();
           $collection->add_features(\@featurelist);

           $collection->features(-attributes =>
                                 [ { 'location' => Bio::Location::Simple->new
                                         (-start=> 1, -end => 300) ,
                                         'overlaps' }]);

DESCRIPTION

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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason@bioperl.org

APPENDIX

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

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

   features
        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.