Raw content of Bio::SeqFeature::CollectionI # $Id: CollectionI.pm,v 1.2 2002/10/22 07:45:20 lapp Exp $ # # BioPerl module for Bio::SeqFeature::CollectionI # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects. =head1 SYNOPSIS # get a Bio::SeqFeature::CollectionI somehow # perhaps a Bio::SeqFeature::Collection use Bio::SeqFeature::Collection; my $collection = new Bio::SeqFeature::Collection; $collection->add_features(\@featurelist); $collection->features(-attributes => [ { 'location' => new Bio::Location::Simple (-start=> 1, -end => 300) , 'overlaps' }]); =head1 DESCRIPTION This interface describes the basic methods needed for a collection of Sequence Features. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::CollectionI; use vars qw(@ISA); use strict; use Carp; use Bio::Root::RootI; @ISA = qw( Bio::Root::RootI ); =head2 add_features Title : add_features Usage : $collection->add_features(\@features); Function: Returns : number of features added Args : arrayref of Bio::SeqFeatureI objects to index =cut sub add_features{ shift->throw_not_implemented(); } =head2 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 L<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. =cut sub features{ shift->throw_not_implemented(); } 1;