/ 
bioperl-0.6.2
/ Bio::Annotation

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->database "\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

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@bio.perl.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 _

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   : $self->add_Reference($ref1[,$ref2,...])
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    :
Title   : add_DBLink
Usage   : $self->add_DBLink($ref)
Function: adds a link object
Example :
Returns : 
Args    :
Title   : each_DBLink
Usage   : foreach $ref ( $self->each_DBlink() )
Function: gets an array of DBlink of objects
Example :
Returns : 
Args    :