Bio::Annotation Reference
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Summary
Bio::Annotation::Reference - Specialised DBLink object for Literature References
Package variables
Privates (from "my" definitions)
$DEFAULT_CB = sub { $_[0]->title || ''}
Inherit
Bio::Annotation::DBLink
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...
Methods
newDescriptionCode
as_textDescriptionCode
display_textDescriptionCode
hash_treeDescriptionCode
startDescriptionCode
endDescriptionCode
rpDescriptionCode
rgDescriptionCode
authorsDescriptionCode
locationDescriptionCode
titleDescriptionCode
medlineDescriptionCode
pubmedDescriptionCode
databaseDescriptionCode
primary_idDescriptionCode
optional_idDescriptionCode
publisherDescriptionCode
editorsDescriptionCode
encoded_refDescriptionCode
doiDescriptionCode
consortiumDescriptionCode
gb_referenceDescriptionCode
Methods description
newcode    nextTop
 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
as_textcodeprevnextTop
 Title   : as_text
Usage :
Function:
Example :
Returns :
Args :
display_textcodeprevnextTop
 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_treecodeprevnextTop
 Title   : hash_tree
Usage :
Function:
Example :
Returns :
Args :
startcodeprevnextTop
 Title   : start
Usage : $self->start($newval)
Function: Gives the reference start base
Example :
Returns : value of start
Args : newvalue (optional)
endcodeprevnextTop
 Title   : end
Usage : $self->end($newval)
Function: Gives the reference end base
Example :
Returns : value of end
Args : newvalue (optional)
rpcodeprevnextTop
 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)
rgcodeprevnextTop
 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)
authorscodeprevnextTop
 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)
locationcodeprevnextTop
 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)
titlecodeprevnextTop
 Title   : title
Usage : $self->title($newval)
Function: Gives the title line (if exists)
Example :
Returns : value of title
Args : newvalue (optional)
medlinecodeprevnextTop
 Title   : medline
Usage : $self->medline($newval)
Function: Gives the medline number
Example :
Returns : value of medline
Args : newvalue (optional)
pubmedcodeprevnextTop
 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)
databasecodeprevnextTop
 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_idcodeprevnextTop
 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_idcodeprevnextTop
 Title   : optional_id
Usage :
Function: Overrides DBLink optional_id to provide the PubMed number.
Example :
Returns :
Args :
publishercodeprevnextTop
 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)
editorscodeprevnextTop
 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_refcodeprevnextTop
 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)
doicodeprevnextTop
 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/>
Example : Returns : value of doi Args : newvalue (optional)
consortiumcodeprevnextTop
 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_referencecodeprevnextTop
 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)
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    my ($start,$end,$authors,$consortium,$location,$title,$medline,
    $pubmed,$rp,$rg,$doi) =
    $self->_rearrange([qw(START
                  END
                  AUTHORS
                  CONSORTIUM
                  LOCATION
                  TITLE
                  MEDLINE
                  PUBMED
                  RP
                  RG
				  DOI
                  )],@args);

    defined $start    && $self->start($start);
    defined $end      && $self->end($end);
    defined $authors  && $self->authors($authors);
    defined $consortium  && $self->consortium($consortium);
    defined $location && $self->location($location);
    defined $title    && $self->title($title);
    defined $medline  && $self->medline($medline);
    defined $pubmed   && $self->pubmed($pubmed);
    defined $rp       && $self->rp($rp);
    defined $rg       && $self->rg($rg);
	defined $doi      && $self->doi($doi);
    return $self;
}
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   # this could get out of hand!
return "Reference: ".$self->title;
}
display_textdescriptionprevnextTop
sub display_text {
    my ($self, $cb) = @_;
    $cb ||= $DEFAULT_CB;
    $self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
    return $cb->($self);
  }
}
hash_treedescriptionprevnextTop
sub hash_tree {
    my ($self) = @_;

    my $h = {};
    $h->{'title'}   = $self->title;
    $h->{'authors'} = $self->authors;
    $h->{'location'} = $self->location;
    if (defined $self->start) {
        $h->{'start'}   = $self->start;
    }
    if (defined $self->end) {
        $h->{'end'} = $self->end;
    }
    $h->{'medline'} = $self->medline;
    if (defined $self->pubmed) {
        $h->{'pubmed'} = $self->pubmed;
    }

    return $h;
}
startdescriptionprevnextTop
sub start {
    my ($self,$value) = @_;
    if( defined $value) {
    $self->{'start'} = $value;
    }
    return $self->{'start'};
}
enddescriptionprevnextTop
sub end {
    my ($self,$value) = @_;
    if( defined $value) {
    $self->{'end'} = $value;
    }
    return $self->{'end'};
}
rpdescriptionprevnextTop
sub rp {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'rp'} = $value;
    }
    return $self->{'rp'};
}
rgdescriptionprevnextTop
sub rg {
    my $self = shift;

    return $self->{'rg'} = shift if @_;
    return $self->{'rg'};
}
authorsdescriptionprevnextTop
sub authors {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'authors'} = $value;
    }
    return $self->{'authors'};
}
locationdescriptionprevnextTop
sub location {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'location'} = $value;
    }
    return $self->{'location'};
}
titledescriptionprevnextTop
sub title {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'title'} = $value;
    }
    return $self->{'title'};
}
medlinedescriptionprevnextTop
sub medline {
    my ($self,$value) = @_;
    if( defined $value) {
    $self->{'medline'} = $value;
    }
    return $self->{'medline'};
}
pubmeddescriptionprevnextTop
sub pubmed {
    my ($self,$value) = @_;
    if( defined $value) {
    $self->{'pubmed'} = $value;
    }
    return $self->{'pubmed'};
}
databasedescriptionprevnextTop
sub database {
    my ($self, @args) = @_;
    my $default = 'MEDLINE';
    if (! defined $self->medline && defined $self->pubmed) {
        $default = 'PUBMED';
    }
    return $self->SUPER::database(@args) || $default;
}
primary_iddescriptionprevnextTop
sub primary_id {
    my ($self, @args) = @_;
    if (@args) {
        $self->medline(@args);
    }
    if (! defined $self->medline && defined $self->pubmed) {
        return $self->pubmed;
    }
    return $self->medline;
}
optional_iddescriptionprevnextTop
sub optional_id {
   my ($self, @args) = @_;

   return $self->pubmed(@args);
}
publisherdescriptionprevnextTop
sub publisher {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'publisher'} = $value;
   }
   return $self->{'publisher'};
}
editorsdescriptionprevnextTop
sub editors {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'editors'} = $value;
   }
   return $self->{'editors'};
}
encoded_refdescriptionprevnextTop
sub encoded_ref {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'encoded_ref'} = $value;
   }
   return $self->{'encoded_ref'};
}
doidescriptionprevnextTop
sub doi {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'doi'} = $value;
    }
    return $self->{'doi'};
}
consortiumdescriptionprevnextTop
sub consortium {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'consortium'} = $value;
    }
    return $self->{'consortium'};
}
gb_referencedescriptionprevnextTop
sub gb_reference {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'gb_reference'} = $value;
    }
    return $self->{'gb_reference'};

}

1;
}
General documentation
AUTHOR - Ewan Birney Top
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
AnnotationI implementing functionsTop
tagnameTop
 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 ReferencesTop