/ 
bioperl-1.0.2
/ 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://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)