Bio::Annotation::Collection(3pm)

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::AnnotationCollectionI

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email [email protected]

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_nested_Annotations

 Title   : get_nested_Annotations
 Usage   : my @annotations = $collection->get_nested_Annotations(
                                '-key' => \@keys,
                                '-recursive => 1);
 Function: Retrieves all the Bio::AnnotationI objects for one or more
           specific key(s). If -recursive is set to true, traverses the nested 
           annotation collections recursively and returns all annotations 
           matching the 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      => arrayref of keys to search for (optional)
           -recursive => boolean, whether or not to recursively traverse the 
            nested annotations and return annotations with matching keys.

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 use a collection as an
   annotation object for an annotation collection.

as_text

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

display_text

 Title   : display_text
 Usage   : my $str = $ann->display_text();
 Function: returns a string. Unlike as_text(), this method returns a string
           formatted as would be expected for te specific implementation.
           One can pass a callback as an argument which allows custom text
           generation; the callback is passed the current instance and any text
           returned
 Example :
 Returns : a string
 Args    : [optional] callback

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    :

add_DBLink

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

each_DBLink

 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)