Ewan Birney

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://bio.perl.org/bioperl-bugs/

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::Annotation::CollectionI 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 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_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);
           $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
 Function: Adds an annotation for a specific 
 Returns : none
 Args    : annotation key ('disease', 'dblink', ...)
           object to store (must be Bio::AnnotationI compliant)
           [optional] object archytype to map future storage of object 
                      of these types to

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)