Christopher Fields > BioPerl-1.6.922 > Bio::SeqFeature::CollectionI



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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924


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.

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