Bio AnnotationCollectionI
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Summary
Bio::AnnotationCollectionI - Interface for annotation collections
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
   # get an AnnotationCollectionI somehow, eg
$ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # also defined hash_tree method, which allows data orientated # access into this object $hash = $value->hash_tree(); } }
Description
Annotation Collections are a way of storing a series of "interesting
facts" about something. We call an "interesting fact" in Bioperl an
Annotation (this differs from a Sequence Feature, which is called
a Sequence Feature and may or may not have an Annotation Collection).
A benefit of this approach is that all sorts of simple, interesting
observations can be collected, the possibility is endless.
The Bioperl approach is that the "interesting facts" are represented by
Bio::AnnotationI objects. The interface Bio::AnnotationI guarantees
two methods
   $obj->as_text(); # string formated to display to users
and
   $obj->hash_tree(); # hash with defined rules for data-orientated discovery
The hash_tree method is designed to play well with XML output and
other "nested-tag-of-data-values", think BoulderIO and/or Ace stuff. For more
information see Bio::AnnotationI.
Annotations are stored in AnnotationCollections, each Annotation under a
different "tag". The tags allow simple discovery of the available annotations,
and in some cases (like the tag "gene_name") indicate how to interpret the
data underneath the tag. The tag is only one tag deep and each tag can have an
array of values.
In addition, AnnotationCollections are guaranteed to maintain consistent
types of objects under each tag - at least that each object complies to one
interface. The "standard" AnnotationCollection insists the following rules
are set up:
  Tag            Object
--- ------
comment Bio::Annotation::Comment
dblink Bio::Annotation::DBLink
description Bio::Annotation::SimpleValue
gene_name Bio::Annotation::SimpleValue
ontology_term Bio::Annotation::OntologyTerm
reference Bio::Annotation::Reference
These tags are the implict tags that the SeqIO system needs to round-trip
GenBank/EMBL/Swissprot.
However, you as a user and us collectively as a community can grow the
"standard" tag mapping over time and specifically for a particular
area.
Methods
get_all_annotation_keysDescriptionCode
get_AnnotationsDescriptionCode
add_AnnotationDescriptionCode
remove_AnnotationsDescriptionCode
get_num_of_annotationsDescriptionCode
Methods description
get_all_annotation_keys()code    nextTop
 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()codeprevnextTop
 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
add_Annotation()codeprevnextTop
 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. 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()codeprevnextTop
 Usage   :
Function: Remove the annotations for the specified key from this collection.
Returns : an list of 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)
get_num_of_annotations()codeprevnextTop
 Usage   : my $count = $collection->get_num_of_annotations()
Function: Returns the count of all annotations stored in this collection
Returns : integer
Args : none
Methods code
get_all_annotation_keysdescriptionprevnextTop
sub get_all_annotation_keys {
    shift->throw_not_implemented();
}
get_AnnotationsdescriptionprevnextTop
sub get_Annotations {
    shift->throw_not_implemented();
}
add_AnnotationdescriptionprevnextTop
sub add_Annotation {
  shift->throw_not_implemented();
}
remove_AnnotationsdescriptionprevnextTop
sub remove_Annotations {
  shift->throw_not_implemented();
}
get_num_of_annotationsdescriptionprevnextTop
sub get_num_of_annotations {
    shift->throw_not_implemented();
}

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 one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org
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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods
are usually preceded with a _
ACCESSOR METHODSTop
Use these for Bio::AnnotationI object access.