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Manual Reference Pages  -  BIO::ANNOTATION::REFERENCE (3)

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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...

AUTHOR - Ewan Birney



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : $ref = Bio::Annotation::Reference->new( -title => title line,
                           -authors => author line,
                           -location => location line,
                           -medline => 9988812);
 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


 Title   : as_text
 Usage   :
 Example :
 Returns :
 Args    :


 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
 Example :
 Returns : a string
 Args    : [optional] callback


 Title   : hash_tree
 Usage   :
 Example :
 Returns :
 Args    :


 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


 Title   : start
 Usage   : $self->start($newval)
 Function: Gives the reference start base
 Example :
 Returns : value of start
 Args    : newvalue (optional)


 Title   : end
 Usage   : $self->end($newval)
 Function: Gives the reference end base
 Example :
 Returns : value of end
 Args    : newvalue (optional)


 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)


 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)


 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)


 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
 Usage   : $self->title($newval)
 Function: Gives the title line (if exists)
 Example :
 Returns : value of title
 Args    : newvalue (optional)


 Title   : medline
 Usage   : $self->medline($newval)
 Function: Gives the medline number
 Example :
 Returns : value of medline
 Args    : newvalue (optional)


 Title   : pubmed
 Usage   : $refobj->pubmed($newval)
 Function: Get/Set the PubMed number, if it is different from the MedLine
 Example :
 Returns : value of medline
 Args    : newvalue (optional)


 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    :


 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    :


 Title   : optional_id
 Usage   :
 Function: Overrides DBLink optional_id to provide the PubMed number.
 Example :
 Returns :
 Args    :


 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)


 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)


 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)


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


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


 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)


 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)

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perl v5.20.3 BIO::ANNOTATION::REFERENCE (3) 2016-04-05

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