/ 
bioperl-0.7.2
/ Bio::Annotation

NAME

Bio::Annotation - A generic object for annotations

SYNOPSIS

use Bio::Annotation;
use Bio::Annotation::DBLink;
use Bio::Annotation::Comment;

my $link = new Bio::Annotation::DBLink(-database => 'TSC',
                                 -primary_id => 'TSC0000030'
                                 );
my $ann = Bio::Annotation->new('-description'  => 'some description');
$ann->add_DBLink($link);

my $comment = Bio::Annotation::Comment->new('-text' => 'Text of comment');
my $comment2 = Bio::Annotation::Comment->new('-text' => 'Second comment');
$ann->add_Comment($comment);
$ann->add_Comment($comment2);

my $ref = Bio::Annotation::Reference->new( '-authors' => 'author line',
                                       '-title'   => 'title line',
                                       '-location'=> 'location line',
                                       '-start'   => 12);
$ann->add_Reference($ref);

# 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";
}

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 _

new

Title   : new
Usage   : $annotation = Bio::Annotation->new( '-description' => 'a description line');
Function: Makes a new Annotation object. The main thing 
          you will want to do with this is add comment objects and
          dblink objects, with calls like

           $annotation->add_Comment($comment);
           $annotation->add_DBLink($dblink);

Example :
Returns : a new Bio::Annotation Object
Args    : hash, potentially with one field, -description

description

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

add_gene_name

Title   : add_gene_name
Usage   : $self->add_gene_name($name1[,$name2,...])
Function: adds a reference object
Example :
Returns : 
Args    : a string, or a list of strings

remove_gene_name

Title   : remove_gene_name
Usage   : $self->remove_gene_name($index)
Function: removes a particular gene name
Example :
Returns : 
Args    : index of the name to remove

each_gene_name

Title   : each_gene_name
Usage   : foreach $genename ( $self->each_gene_name() ) {
              print "seq has gene name $genename\n";
          }
Function: gets the array of gene names
Example :
Returns : an array of strings
Args    :

add_Reference

Title   : add_Reference
Usage   : $self->add_Reference($ref1[,$ref2,...])
Function: adds a reference object
Example :
Returns : 
Args    : a Bio::Annotation::Reference or derived object

remove_Reference

Title   : remove_Reference
Usage   : $self->remove_Reference($index)
Function: removes a reference object
Example :
Returns : 
Args    : index number from references array

each_Reference

Title   : each_Reference
Usage   : foreach $ref ( $self->each_Reference() )
Function: gets an array of reference
Example :
Returns : an array of Bio::Annotation::Reference or derived objects
Args    :

add_Comment

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

remove_Comment

Title   : remove_Comment
Usage   : $self->remove_Comment($index)
Function: removes a comment object
Example :
Returns : 
Args    : index number from comments array

each_Comment

Title   : each_Comment
Usage   : foreach $ref ( $self->each_Comment() )
Function: gets an array of Comment of objects
Example :
Returns : an array of Bio::Annotation::Comment or derived objects
Args    : none
Title   : add_DBLink
Usage   : $self->add_DBLink($ref)
Function: adds a link object
Example :
Returns : 
Args    : a Bio::Annotation::DBLink or derived object
Title   : remove_DBLink
Usage   : $self->remove_DBLink($index)
Function: removes a DBLink object
Example :
Returns : 
Args    : index number from links array
Title   : each_DBLink
Usage   : foreach $ref ( $self->each_DBlink() )
Function: gets an array of DBlink of objects
Example :
Returns : an array of Bio::Annotation::DBlink or derived objects
Args    :