/ 
bioperl-1.2.3
/ Bio::SeqFeature::CollectionI

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


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

DESCRIPTION

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

FEEDBACK

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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.

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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:

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http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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.