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
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AUTHOR - Jason Stajich
Email [email protected]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.