/ 
bioperl-1.2.2
/ Bio::Annotation::Reference

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    :

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)

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)