Bio::SeqFeature::CollectionI(3pm) User Contributed Perl Documentation 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
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:
https://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 Bio::SeqFeature::CollectionI(3pm)