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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    :
 
 

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 explicitely 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)
 
 

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)