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BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqFeature::AnnotationAdaptor

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->get_tag_values("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://github.com/bioperl/bioperl-live/issues

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)