/ 
bioperl-0.6
/ Bio::Annotation::Reference

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)

comment

Title   : comment
Usage   : $obj->comment($newval)
Function: 
Example : 
Returns : value of comment
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, unless it indicates
          start and end reference bases
Example : 
Returns : value of rp
Args    : newvalue (optional)