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.