Bio::Annotation::Reference(3pm) 			User Contributed Perl Documentation			   Bio::Annotation::Reference(3pm)

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...

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

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, pubmed,
		  start, end, consortium, rp and rg attributes

AnnotationI implementing functions
   as_text
	Title	: as_text
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   display_text
	Title	: display_text
	Usage	: my $str = $ann->display_text();
	Function: returns a string. Unlike as_text(), this method returns a string
		  formatted as would be expected for te specific implementation.

		  One can pass a callback as an argument which allows custom text
		  generation; the callback is passed the current instance and any text
		  returned
	Example :
	Returns : a string
	Args	: [optional] callback

   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)

   rg
	Title	: rg
	Usage	: $obj->rg($newval)
	Function: Gives the RG line. This is Swissprot/Uniprot specific, and
		  if set will usually be identical to the authors attribute,
		  but the swissprot manual does allow both RG and RA (author)
		  to be present for the same reference.

	Example :
	Returns : value of rg (a scalar)
	Args	: on set, new value (a scalar or undef, 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' (or 'PUBMED'
		  if only pubmed id has been supplied), unless the database has been
		  set explicitly before.
	Example :
	Returns :
	Args	:

   primary_id
	Title	: primary_id
	Usage	:
	Function: Overrides DBLink primary_id to provide medline number, or pubmed
		  number if only that has been defined
	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)

   doi
	Title	: doi
	Usage	: $self->doi($newval)
	Function: Gives the DOI (Digital Object Identifier) from the International
		  DOI Foundation (http://www.doi.org/), which can be used to resolve
			  URL links for the full-text documents using:

			  http://dx.doi.org/<doi>

	Example :
	Returns : value of doi
	Args	: newvalue (optional)

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

   gb_reference
	Title	: gb_reference
	Usage	: $obj->gb_reference($newval)
	Function: Gives the generic GenBank REFERENCE line. This is GenBank-specific.
		  If set, this includes everything on the reference line except
			  the REFERENCE tag and the reference count.  This is mainly a
			  fallback for the few instances when REFERENCE lines have unusual
			  additional information such as split sequence locations, feature
			  references, etc.  See Bug 2020 in Bugzilla for more information.
	Example :
	Returns : value of gb_reference (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.2							    2012-03-02					   Bio::Annotation::Reference(3pm)