/ 
bioperl-1.2.3
/ Bio::Annotation::Collection

NAME

Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI

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

Bioperl implementation for Bio::AnnotationCollecitonI

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 one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org              - General discussion
http://bio.perl.org/MailList.html  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : $coll = Bio::Annotation::Collection->new()
Function: Makes a new Annotation::Collection object. 
Returns : Bio::Annotation::Collection
Args    : none

Bio::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 one or more
          specific key(s).

          If no key is given, returns all annotation objects.

          The returned objects will have their tagname() attribute set to
          the key under which they were attached, unless the tagname was
          already set.

Returns : list of Bio::AnnotationI - empty if no objects stored for a key
Args    : keys (list of strings) for annotations (optional)

get_all_Annotations

Title   : get_all_Annotations
Usage   :
Function: Similar to get_Annotations, but traverses and flattens nested
          annotation collections. This means that collections in the
          tree will be replaced by their components.

          Keys will not be passed on to nested collections. I.e., if the
          tag name of a nested collection matches the key, it will be
          flattened in its entirety.

          Hence, for un-nested annotation collections this will be identical
          to get_Annotations.
Example :
Returns : an array of L<Bio::AnnotationI> compliant objects
Args    : keys (list of strings) for annotations (optional)

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 - mainly for 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.

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.
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)

flatten_Annotations

Title   : flatten_Annotations
Usage   :
Function: Flattens part or all of the annotations in this collection.

          This is a convenience method for getting the flattened
          annotation for the given keys, removing the annotation for
          those keys, and adding back the flattened array.

          This should not change anything for un-nested collections.
Example :
Returns : an array Bio::AnnotationI compliant objects which were stored
          under the given key(s)
Args    : list of keys (strings) the annotation for which to flatten,
          defaults to all keys if not given

Bio::AnnotationI methods implementations

This is to allow nested annotation: you can a collection as an
annotation object to an annotation collection.

as_text

Title   : as_text
Usage   :
Function: See L<Bio::AnnotationI>
Example :
Returns : a string
Args    : none

hash_tree

Title   : hash_tree
Usage   :
Function: See L<Bio::AnnotationI>
Example :
Returns : a hash reference
Args    : none

tagname

Title   : tagname
Usage   : $obj->tagname($newval)
Function: Get/set the tagname for this annotation value.

          Setting this is optional. If set, it obviates the need to
          provide a tag to Bio::AnnotationCollectionI when adding
          this object. When obtaining an AnnotationI object from the
          collection, the collection will set the value to the tag
          under which it was stored unless the object has a tag
          stored already.

Example : 
Returns : value of tagname (a scalar)
Args    : new value (a scalar, optional)

Backward compatible functions

Functions put in for backward compatibility with old Bio::Annotation.pm stuff

description

Title   : description
Usage   :
Function:
Example :
Returns : 
Args    :

add_gene_name

Title   : add_gene_name
Usage   :
Function:
Example :
Returns : 
Args    :

each_gene_name

Title   : each_gene_name
Usage   :
Function:
Example :
Returns : 
Args    :

add_Reference

Title   : add_Reference
Usage   :
Function:
Example :
Returns : 
Args    :

each_Reference

Title   : each_Reference
Usage   :
Function:
Example :
Returns : 
Args    :

add_Comment

Title   : add_Comment
Usage   :
Function:
Example :
Returns : 
Args    :

each_Comment

Title   : each_Comment
Usage   :
Function:
Example :
Returns : 
Args    :
Title   : add_DBLink
Usage   :
Function:
Example :
Returns : 
Args    :
Title   : each_DBLink
Usage   :
Function:
Example :
Returns : 
Args    :

Implementation management functions

_typemap

Title   : _typemap
Usage   : $obj->_typemap($newval)
Function: 
Example : 
Returns : value of _typemap
Args    : newvalue (optional)