Bio::Annotation::Reference - Specialised DBLink object for Literature References $reg = Bio::Annotation::Reference->new( -title => 'title line', -location => 'location line', -authors => 'author line', -medline => 998122 ); 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... Describe contact details here 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

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

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

tagname
Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional)

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)