Provided by: libbio-perl-perl_1.7.2-3_all bug

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)