Bio::SeqFeature::ColleUsernContributed Perl DocBio::SeqFeature::CollectionI(3)NAMEBio::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:
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.
perl v5.14.1 2011-07-22 Bio::SeqFeature::CollectionI(3)
