NAME

Bio::Annotation::Reference - Literature Reference Block

SYNOPSIS

    $annotation = $seq->annotation();
    foreach $ref ( $annotation->each_Reference() ) {
        print "Title: ",$ref->title,"\n";
        print "Authors:",$ref->authors,"\n";
        print "Location:",$ref->location,"\n";
    }

    

DESCRIPTION

Object which presents a literature reference. This is considered to be a specialised form of database link. The literature reference contains the title, authors and location lines as text: no attempt is made to parse these into more computationally accessibly aspects, as it becomes a nightmare. A slot for the medline accession number is also provided.

As most people will realise this object is really designed to supported literature references made in flat files. For more complex representations, including abstract and possibly full text a richer object that can somehow be easily connected (? inheritence or composition) to this object would be ideal. Please air your views on the guts list and if possible, nominate yourself as someone who can do this.

CONTACT

Ewan Birney <birney@ebi.ac.uk>

APPENDIX

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

authors

 Title   : authors
 Usage   : $self->authors($newval)
 Function: Gives the author line. No attempt is made to parse the author line
 Example : 
 Returns : value of authors
 Args    : newvalue (optional)

location

 Title   : location
 Usage   : $self->location($newval)
 Function: Gives the location line. No attempt is made to parse the location line
 Example : 
 Returns : value of location
 Args    : newvalue (optional)

title

 Title   : title
 Usage   : $self->title($newval)
 Function: Gives the title line (if exists)
 Example : 
 Returns : value of title
 Args    : newvalue (optional)

medline

 Title   : medline
 Usage   : $self->medline($newval)
 Function: Gives the medline number
 Example : 
 Returns : value of medline
 Args    : newvalue (optional)

database

 Title   : database
 Usage   :
 Function: Overrides DBLink database to be hard coded to 'MEDLINE'
 Example :
 Returns : 
 Args    :

primary_id

 Title   : primary_id
 Usage   :
 Function: Overrides DBLink primary_id to provide medline number
 Example :
 Returns : 
 Args    :

start

 Title   : start
 Usage   : $self->start($newval)
 Function: Gives the reference start base
 Example : 
 Returns : value of start
 Args    : newvalue (optional)

end

 Title   : end
 Usage   : $self->end($newval)
 Function: Gives the reference end base 
 Example : 
 Returns : value of end
 Args    : newvalue (optional)

rp

 Title   : rp
 Usage   : $self->rp($newval)
 Function: Gives the RP line. No attempt is made to parse this line.
 Example : 
 Returns : value of rp
 Args    : newvalue (optional)