NAME

Bio::Annotation - A generic object for annotations

SYNOPSIS

    # get an annotation somehow in $ann

    # description is a simple, one line description 
    print "Description is ",$ann->description "\n";


    foreach $comment ( $ann->each_Comment ) {
       # $comment is a Bio::Annotation::Comment object
          print "Comment: ", $comment->text(), "\n"
       }
    }

    foreach $link ( $ann->each_DBLink ) {
       # link is a Bio::Annotation::DBLink object
       print "Link to ",$link->primary_id, " in database", $link->db "\n";
    }

    foreach $ref ( $ann->each_Reference ) {
       # link is a Bio::Annotation::Reference object
       print "Reference title ", $ref->title , "\n";
    }

    #
    # Making an annotation object from scratch
    #

    $ann = Bio::Pfam::Annotation->new();

    $ann->description("Description text");
    print "Annotation description is ", $ann->description, "\n";
   

DESCRIPTION

The object represents generic biological annotation of an object. It has the ability to provide

    a brief, one line description
    free text comments
    links to other biological objects
    references to literature

It does not have the following abilities

    The basis (experimental/non experimental/homology) 
       of the annotation. This is considered to be part of
       the object which owns the annotation. This is 
       because the type of relevant basis is usually 
       dependent on the object

    The previous revisions of the object
       This should be a property of whatever database this
       object comes from

CONTACT

Mail birney@sanger.ac.uk with any queries

APPENDIX

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

description

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

gene_name

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

add_Reference

 Title   : add_Reference
 Usage   : $self->add_Reference($ref)
 Function: adds a reference object
 Example :
 Returns : 
 Args    :

each_Reference

 Title   : each_Reference
 Usage   : foreach $ref ( $self->each_Reference() )
 Function: gets an array of reference
 Example :
 Returns : 
 Args    :

add_Comment

 Title   : add_Comment
 Usage   : $self->add_Comment($ref)
 Function: adds a Comment object
 Example :
 Returns : 
 Args    :

each_Comment

 Title   : each_Comment
 Usage   : foreach $ref ( $self->each_Comment() )
 Function: gets an array of Comment of objects
 Example :
 Returns : 
 Args    :

add_DBLink

 Title   : add_DBLink
 Usage   : $self->add_DBLink($ref)
 Function: adds a link object
 Example :
 Returns : 
 Args    :

each_DBLink

 Title   : each_DBLink
 Usage   : foreach $ref ( $self->each_DBlink() )
 Function: gets an array of DBlink of objects
 Example :
 Returns : 
 Args    :