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://github.com/bioperl/bioperl-live/issues
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.