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Bio::SeqFeature::CollectionI.3pm

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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

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.