Bio::SeqFeature CollectionI
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Summary
Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::Root::RootI
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.
Methods
add_featuresDescriptionCode
featuresDescriptionCode
Methods description
add_featurescode    nextTop
 Title   : add_features
Usage : $collection->add_features(\@features);
Function:
Returns : number of features added
Args : arrayref of Bio::SeqFeatureI objects to index
featurescodeprevnextTop
 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.
Methods code
add_featuresdescriptionprevnextTop
sub add_features {
    shift->throw_not_implemented();
}
featuresdescriptionprevnextTop
sub features {
    shift->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _