Bio::SeqFeature::AnnotationAdaptor(3pm) 		User Contributed Perl Documentation		   Bio::SeqFeature::AnnotationAdaptor(3pm)

NAME

       Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation

SYNOPSIS

	  use Bio::SeqFeature::Generic;
	  use Bio::SeqFeature::AnnotationAdaptor;

	  # obtain a SeqFeatureI implementing object somehow
	  my $feat = Bio::SeqFeature::Generic->new(-start => 10, -end => 20);

	  # add tag/value annotation
	  $feat->add_tag_value("mytag", "value of tag mytag");
	  $feat->add_tag_value("mytag", "another value of tag mytag");

	  # Bio::SeqFeature::Generic also provides annotation(), which returns a
	  # Bio::AnnotationCollectionI compliant object
	  $feat->annotation->add_Annotation("dbxref", $dblink);

	  # to integrate tag/value annotation with AnnotationCollectionI
	  # annotation, use this adaptor, which also implements
	  # Bio::AnnotationCollectionI
	  my $anncoll = Bio::SeqFeature::AnnotationAdaptor->new(-feature => $feat);

	  # this will now return tag/value pairs as
	  # Bio::Annotation::SimpleValue objects
	  my @anns = $anncoll->get_Annotations("mytag");
	  # other added before annotation is available too
	  my @dblinks = $anncoll->get_Annotations("dbxref");

	  # also supports transparent adding of tag/value pairs in
	  # Bio::AnnotationI flavor
	  my $tagval = Bio::Annotation::SimpleValue->new(-value => "some value",
							 -tagname => "some tag");
	  $anncoll->add_Annotation($tagval);
	  # this is now also available from the feature's tag/value system
	  my @vals = $feat->each_tag_value("some tag");

DESCRIPTION

       Bio::SeqFeatureI defines light-weight annotation of features through tag/value pairs. Conversely, Bio::AnnotationCollectionI together with
       Bio::AnnotationI defines an annotation bag, which is better typed, but more heavy-weight because it contains every single piece of
       annotation as objects. The frequently used base implementation of Bio::SeqFeatureI, Bio::SeqFeature::Generic, defines an additional slot
       for AnnotationCollectionI-compliant annotation.

       This adaptor provides a Bio::AnnotationCollectionI compliant, unified, and integrated view on the annotation of Bio::SeqFeatureI objects,
       including tag/value pairs, and annotation through the annotation() method, if the object supports it. Code using this adaptor does not need
       to worry about the different ways of possibly annotating a SeqFeatureI object, but can instead assume that it strictly follows the
       AnnotationCollectionI scheme. The price to pay is that retrieving and adding annotation will always use objects instead of light-weight
       tag/value pairs.

       In other words, this adaptor allows us to keep the best of both worlds. If you create tens of thousands of feature objects, and your only
       annotation is tag/value pairs, you are best off using the features' native tag/value system. If you create a smaller number of features,
       but with rich and typed annotation mixed with tag/value pairs, this adaptor may be for you. Since its implementation is by double-
       composition, you only need to create one instance of the adaptor. In order to transparently annotate a feature object, set the feature
       using the feature() method. Every annotation you add will be added to the feature object, and hence will not be lost when you set feature()
       to the next object.

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 - Hilmar Lapp
       Email hlapp at gmx.net

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::SeqFeature::AnnotationAdaptor->new();
	Function: Builds a new Bio::SeqFeature::AnnotationAdaptor object
	Returns : an instance of Bio::SeqFeature::AnnotationAdaptor
	Args	: Named parameters
		   -feature    the Bio::SeqFeatureI implementing object to adapt
			       (mandatory to be passed here, or set via feature()
			       before calling other methods)
		   -annotation the Bio::AnnotationCollectionI implementing object
			       for storing richer annotation (this will default to
			       the $feature->annotation() if it supports it)
		   -tagvalue_factory the object factory to use for creating tag/value
			       pair representing objects

   feature
	Title	: feature
	Usage	: $obj->feature($newval)
	Function: Get/set the feature that this object adapts to an
		  AnnotationCollectionI.
	Example :
	Returns : value of feature (a Bio::SeqFeatureI compliant object)
	Args	: new value (a Bio::SeqFeatureI compliant object, optional)

   annotation
	Title	: annotation
	Usage	: $obj->annotation($newval)
	Function: Get/set the AnnotationCollectionI implementing object used by
		  this adaptor to store additional annotation that cannot be stored
		  by the SeqFeatureI itself.

		  If requested before having been set, the value will default to the
		  annotation object of the feature if it has one.
	Example :
	Returns : value of annotation (a Bio::AnnotationCollectionI compliant object)
	Args	: new value (a Bio::AnnotationCollectionI compliant object, optional)

AnnotationCollectionI implementing methods
   get_all_annotation_keys
	Title	: get_all_annotation_keys
	Usage	: $ac->get_all_annotation_keys()
	Function: gives back a list of annotation keys, which are simple text strings
	Returns : list of strings
	Args	: none

   get_Annotations
	Title	: get_Annotations
	Usage	: my @annotations = $collection->get_Annotations('key')
	Function: Retrieves all the Bio::AnnotationI objects for a specific key
	Returns : list of Bio::AnnotationI - empty if no objects stored for a key
	Args	: string which is key for annotations

   get_num_of_annotations
	Title	: get_num_of_annotations
	Usage	: my $count = $collection->get_num_of_annotations()
	Function: Returns the count of all annotations stored in this collection
	Returns : integer
	Args	: none

Implementation specific functions - to allow adding
   add_Annotation
	Title	: add_Annotation
	Usage	: $self->add_Annotation('reference',$object);
		  $self->add_Annotation($object,'Bio::MyInterface::DiseaseI');
		  $self->add_Annotation($object);
		  $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
	Function: Adds an annotation for a specific key.

		  If the key is omitted, the object to be added must provide a value
		  via its tagname().

		  If the archetype is provided, this and future objects added under
		  that tag have to comply with the archetype and will be rejected
		  otherwise.

		  This implementation will add all Bio::Annotation::SimpleValue
		  objects to the adapted features as tag/value pairs. Caveat: this
		  may potentially result in information loss if a derived object
		  is supplied.

	Returns : none
	Args	: annotation key ('disease', 'dblink', ...)
		  object to store (must be Bio::AnnotationI compliant)
		  [optional] object archetype to map future storage of object
			     of these types to

   remove_Annotations
	Title	: remove_Annotations
	Usage	:
	Function: Remove the annotations for the specified key from this
		  collection.

		  If the key happens to be a tag, then the tag is removed
		  from the feature.

	Example :
	Returns : an array Bio::AnnotationI compliant objects which were stored
		  under the given key(s)
	Args	: the key(s) (tag name(s), one or more strings) for which to
		  remove annotations (optional; if none given, flushes all
		  annotations)

Additional methods
   tagvalue_object_factory
	Title	: tagvalue_object_factory
	Usage	: $obj->tagval_object_factory($newval)
	Function: Get/set the object factory to use for creating objects that
		  represent tag/value pairs (e.g.,
		  Bio::Annotation::SimpleValue).

		  The object to be created is expected to follow
		  Bio::Annotation::SimpleValue in terms of supported
		  arguments at creation time, and the methods.

	Example :
	Returns : A Bio::Factory::ObjectFactoryI compliant object
	Args	: new value (a Bio::Factory::ObjectFactoryI compliant object,
		  optional)

perl v5.14.2							    2012-03-02				   Bio::SeqFeature::AnnotationAdaptor(3pm)