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
Inherit
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.
Methods
Methods description
Title : add_features
Usage : $collection->add_features(\@features);
Function:
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. |
Methods code
sub add_features
{ shift->throw_not_implemented(); } | sub features
{ shift->throw_not_implemented();
}
1; } | General documentation
User feedback is an integral part of the evolution of this and other
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| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _