Bio::SeqFeature AnnotationAdaptor
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation
Package variables
No package variables defined.
Included modules
Bio::Annotation::SimpleValue
Inherit
Bio::AnnotatableI Bio::AnnotationCollectionI Bio::Root::Root
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.
Methods
newDescriptionCode
featureDescriptionCode
annotationDescriptionCode
get_all_annotation_keysDescriptionCode
get_AnnotationsDescriptionCode
get_num_of_annotationsDescriptionCode
add_AnnotationDescriptionCode
remove_AnnotationsDescriptionCode
tagvalue_object_factoryDescriptionCode
Methods description
newcode    nextTop
 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
featurecodeprevnextTop
 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)
annotationcodeprevnextTop
 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)
get_all_annotation_keyscodeprevnextTop
 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_AnnotationscodeprevnextTop
 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_annotationscodeprevnextTop
 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
add_AnnotationcodeprevnextTop
 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_AnnotationscodeprevnextTop
 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)
tagvalue_object_factorycodeprevnextTop
 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)
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  my ($feat,$anncoll,$fact) =
	$self->_rearrange([qw(FEATURE
                          ANNOTATION
                          TAGVALUE_FACTORY)], @args);

  $self->feature($feat) if $feat;
  $self->annotation($anncoll) if $feat;
  $self->tagvalue_object_factory($fact) if $fact;

  return $self;
}
featuredescriptionprevnextTop
sub feature {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'feature'} = $value;
    }
    return $self->{'feature'};
}
annotationdescriptionprevnextTop
sub annotation {
    my ($self,$value) = @_;

    if( defined $value) {
        $self->{'annotation'} = $value;
    }
    if((! exists($self->{'annotation'})) &&
       $self->feature()->can('annotation')) {
        return $self->feature()->annotation();
    }
    return $self->{'annotation'};
}
get_all_annotation_keysdescriptionprevnextTop
sub get_all_annotation_keys {
    my ($self) = @_;
    my @keys = ();
    
    # get the tags from the feature object
if ($self->feature()->can('get_all_tags')) { push(@keys, $self->feature()->get_all_tags()); } else { push(@keys, $self->feature()->all_tags()); } # ask the annotation implementation in addition, while avoiding duplicates
if($self->annotation()) { push(@keys, grep { ! $self->feature->has_tag($_); } $self->annotation()->get_all_annotation_keys()); } # done
return @keys;
}
get_AnnotationsdescriptionprevnextTop
sub get_Annotations {
    my ($self, @keys) = @_;
    my @anns = ();

    # we need a annotation object factory
my $fact = $self->tagvalue_object_factory(); # get all tags if no keys have been provided
@keys = $self->feature->all_tags() unless @keys; # build object for each value for each tag
foreach my $key (@keys) { # protect against keys that aren't tags
next unless $self->feature->has_tag($key); # add each tag/value pair as a SimpleValue object
foreach my $val ($self->feature()->get_tag_values($key)) { my $ann; if($fact) { $ann = $fact->create_object(-value => $val, -tagname => $key); } else { $ann = Bio::Annotation::SimpleValue->new(-value => $val, -tagname => $key); } push(@anns, $ann); } } # add what is in the annotation implementation if any
if($self->annotation()) { push(@anns, $self->annotation->get_Annotations(@keys)); } # done
return @anns;
}
get_num_of_annotationsdescriptionprevnextTop
sub get_num_of_annotations {
  my ($self) = @_;

  # first, count the number of tags on the feature
my $num_anns = 0; foreach ($self->feature()->all_tags()) { $num_anns += scalar( $self->feature()->get_tag_values($_)); } # add from the annotation implementation if any
if($self->annotation()) { $num_anns += $self->annotation()->get_num_of_annotations(); } # done
return $num_anns;
}
add_AnnotationdescriptionprevnextTop
sub add_Annotation {
    my ($self,$key,$object,$archetype) = @_;
   
    # if there's no key we use the tagname() as key
if(ref($key) && $key->isa("Bio::AnnotationI") && (! ($object && ref($object)))) { $archetype = $object if $object; $object = $key; $key = $object->tagname(); $key = $key->name() if $key && ref($key); # OntologyTermI
$self->throw("Annotation object must have a tagname if key omitted") unless $key; } if( !defined $object ) { $self->throw("Must have at least key and object in add_Annotation"); } if( ! (ref($object) && $object->isa("Bio::AnnotationI")) ) { $self->throw("object must be a Bio::AnnotationI compliant object, otherwise we wont add it!"); } # ready to add -- if it's a SimpleValue, we add to the feature's tags,
# otherwise we'll add to the annotation collection implementation
if($object->isa("Bio::Annotation::SimpleValue") && $self->feature()->can('add_tag_value')) { return $self->feature()->add_tag_value($key, $object->value()); } else { my $anncoll = $self->annotation(); if(! $anncoll) { $anncoll = Bio::Annotation::Collection->new(); $self->annotation($anncoll); } if($anncoll->can('add_Annotation')) { return $anncoll->add_Annotation($key,$object,$archetype); } $self->throw("Annotation implementation does not allow adding!"); }
}
remove_AnnotationsdescriptionprevnextTop
sub remove_Annotations {
    my ($self, @keys) = @_;

    # set to all keys if none are supplied
@keys = $self->get_all_annotation_keys() unless @keys; # collect existing annotation
my @anns = $self->get_Annotations(@keys); # flush
foreach my $key (@keys) { # delete the tag if it is one
$self->feature->remove_tag($key) if $self->feature->has_tag($key); # and delegate to the annotation implementation
my $anncoll = $self->annotation(); if($anncoll && $anncoll->can('remove_Annotations')) { $anncoll->remove_Annotations($key); } elsif($anncoll) { $self->warn("Annotation bundle implementation ".ref($anncoll). " does not allow remove!"); } } return @anns;
}
tagvalue_object_factorydescriptionprevnextTop
sub tagvalue_object_factory {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'tagval_object_factory'} = $value;
    }
    return $self->{'tagval_object_factory'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
AnnotationCollectionI implementing methodsTop
Implementation specific functions - to allow addingTop
Additional methodsTop