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BioPerl-1.007000_006
River stage two • 60 direct dependents • 65 total dependents
/ 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...

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)