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 = new Bio::SeqFeature::Collection; $collection->add_features(\@featurelist); $collection->features(-attributes => [ { 'location' => new Bio::Location::Simple (-start=> 1, -end => 300) , 'overlaps' }]); This interface describes the basic methods needed for a collection of Sequence Features.

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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/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here 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.