Bio::Annotation
Reference
Summary
Bio::Annotation::Reference - Specialised DBLink object for Literature References
Package variables
No package variables defined.
Included modules
Inherit
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
Methods description
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, start and end
attributes |
Title : as_text
Usage :
Function:
Example :
Returns :
Args : |
Title : hash_tree
Usage :
Function:
Example :
Returns :
Args : |
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
number.
Example :
Returns : value of medline
Args : newvalue (optional) |
Title : database
Usage :
Function: Overrides DBLink database to be hard coded to 'MEDLINE', unless
the database has been set explicitely before.
Example :
Returns :
Args : |
Title : primary_id
Usage :
Function: Overrides DBLink primary_id to provide medline number
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) |
Methods code
sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($start,$end,$authors,$location,$title,$medline,
$pubmed,$rp,$rg) =
$self->_rearrange([qw(START
END
AUTHORS
LOCATION
TITLE
MEDLINE
PUBMED
RP
RG
)],@args);
defined $start && $self->start($start);
defined $end && $self->end($end);
defined $authors && $self->authors($authors);
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);
return $self;} | sub as_text
{ my ($self) = @_;
return "Reference: ".$self->title; } | sub hash_tree
{ my ($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;
return $h;} | sub start
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'start'} = $value;
}
return $self->{'start'};} | sub end
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'end'} = $value;
}
return $self->{'end'};} | sub rp
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'rp'} = $value;
}
return $self->{'rp'};} | sub rg
{ my $self = shift;
return $self->{'rg'} = shift if @_;
return $self->{'rg'};} | sub authors
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'authors'} = $value;
}
return $self->{'authors'};} | sub location
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'location'} = $value;
}
return $self->{'location'};} | sub title
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'title'} = $value;
}
return $self->{'title'};} | sub medline
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'medline'} = $value;
}
return $self->{'medline'};} | sub pubmed
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'pubmed'} = $value;
}
return $self->{'pubmed'};} | sub database
{ my ($self, @args) = @_;
return $self->SUPER::database(@args) || 'MEDLINE'; } | sub primary_id
{ my ($self, @args) = @_;
return $self->medline(@args); } | sub optional_id
{ my ($self, @args) = @_;
return $self->pubmed(@args); } | sub publisher
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'publisher'} = $value;
}
return $self->{'publisher'};} | sub editors
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'editors'} = $value;
}
return $self->{'editors'};} | sub encoded_ref
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'encoded_ref'} = $value;
}
return $self->{'encoded_ref'};} | General documentation
Describe contact details here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
| AnnotationI implementing functions | Top |
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 | Top |