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Bio::SeqFeature::ColleUsernContributed Perl DocBio::SeqFeature::CollectionI(3)

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.

perl v5.32.0			  2019-12-07   Bio::SeqFeature::CollectionI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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