Bio::SeqFeature::AnnotationAdaptor.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)