Ewan Birney

NAME

Bio::Annotation::Reference - Specialised DBLink object for Literature References

SYNOPSIS

    $reg = Bio::Annotation::Reference->new( -title => 'title line',
                                            -location => 'location line',
                                            -authors => 'author line',
                                            -medline => 998122 );

DESCRIPTION

Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (ie, journal page) and authors line.

There is no attempt to do anything more than store these things as strings for processing elsewhere. This is mainly because parsing these things suck and generally are specific to the specific format one is using. To provide an easy route to go format --> object --> format without losing data, we keep them as strings. Feel free to post the list for a better solution, but in general this gets very messy very fast...

CONTACT

Describe contact details here

APPENDIX

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

new

 Title   : new
 Usage   : $ref = Bio::Annotation::Reference->new( -title => 'title line',
                                                   -authors => 'author line',
                                                   -location => 'location line',
                                                   -medline => 9988812);
 Function:
 Example :
 Returns : a new Bio::Annotation::Reference object
 Args    : a hash with optional title, authors, location, medline, start and end
           attributes

AnnotationI implementing functions

as_text

 Title   : as_text
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

hash_tree

 Title   : hash_tree
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

Specific accessors for References

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)

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)

pubmed

 Title   : pubmed
 Usage   : $refobj->pubmed($newval)
 Function: Get/Set the PubMed number, if it is different from 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', unless
           the database has been set explicitely before.
 Example :
 Returns : 
 Args    :

primary_id

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

optional_id

 Title   : optional_id
 Usage   :
 Function: Overrides DBLink optional_id to provide the PubMed number.
 Example :
 Returns : 
 Args    :

publisher

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

editors

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

encoded_ref

 Title   : encoded_ref
 Usage   : $self->encoded_ref($newval)
 Function: Gives the encoded_ref line. No attempt is made to parse the encoded_ref line
        (this is added for reading PDB records (REFN record), where this contains
         ISBN/ISSN/ASTM code)
 Example : 
 Returns : value of encoded_ref
 Args    : newvalue (optional)