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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.

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

   http://bugzilla.open-bio.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_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)