Raw content of Bio::Annotation::Reference
<![CDATA[# $Id: Reference.pm,v 1.18 2002/09/25 18:11:33 lapp Exp $
#
# BioPerl module for Bio::Annotation::Reference
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Annotation::Reference - Specialised DBLink object for Literature References
=head1 SYNOPSIS
$reg = Bio::Annotation::Reference->new( -title => 'title line',
-location => 'location line',
-authors => 'author line',
-medline => 998122 );
=head1 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 --E<gt> object --E<gt> 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...
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Annotation::Reference;
use vars qw(@ISA);
use strict;
use Bio::Annotation::DBLink;
use Bio::AnnotationI;
@ISA = qw(Bio::Annotation::DBLink);
=head2 new
Title : new
Usage : $ref = Bio::Annotation::Reference->new( -title => 'title line',
-authors => 'author line',
-location => 'location line',
-medline => 9988812);
Function:
Example :
Returns : a new Bio::Annotation::Reference object
Args : a hash with optional title, authors, location, medline, start and end
attributes
=cut
sub new{
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($start,$end,$authors,$location,$title,$medline,$tag) =
$self->_rearrange([qw(START
END
AUTHORS
LOCATION
TITLE
MEDLINE
TAGNAME
)],@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 $tag && $self->tagname($tag);
return $self;
}
=head1 AnnotationI implementing functions
=cut
=head2 as_text
Title : as_text
Usage :
Function:
Example :
Returns :
Args :
=cut
sub as_text{
my ($self) = @_;
# this could get out of hand!
return "Reference: ".$self->title;
}
=head2 hash_tree
Title : hash_tree
Usage :
Function:
Example :
Returns :
Args :
=cut
sub hash_tree{
my ($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;
}
=head2 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)
=cut
sub tagname{
my ($self,$value) = @_;
if( defined $value) {
$self->{'tagname'} = $value;
}
return $self->{'tagname'};
}
=head1 Specific accessors for References
=cut
=head2 start
Title : start
Usage : $self->start($newval)
Function: Gives the reference start base
Example :
Returns : value of start
Args : newvalue (optional)
=cut
sub start {
my ($self,$value) = @_;
if( defined $value) {
$self->{'start'} = $value;
}
return $self->{'start'};
}
=head2 end
Title : end
Usage : $self->end($newval)
Function: Gives the reference end base
Example :
Returns : value of end
Args : newvalue (optional)
=cut
sub end {
my ($self,$value) = @_;
if( defined $value) {
$self->{'end'} = $value;
}
return $self->{'end'};
}
=head2 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)
=cut
sub rp{
my ($self,$value) = @_;
if( defined $value) {
$self->{'rp'} = $value;
}
return $self->{'rp'};
}
=head2 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)
=cut
sub authors{
my ($self,$value) = @_;
if( defined $value) {
$self->{'authors'} = $value;
}
return $self->{'authors'};
}
=head2 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)
=cut
sub location{
my ($self,$value) = @_;
if( defined $value) {
$self->{'location'} = $value;
}
return $self->{'location'};
}
=head2 title
Title : title
Usage : $self->title($newval)
Function: Gives the title line (if exists)
Example :
Returns : value of title
Args : newvalue (optional)
=cut
sub title{
my ($self,$value) = @_;
if( defined $value) {
$self->{'title'} = $value;
}
return $self->{'title'};
}
=head2 medline
Title : medline
Usage : $self->medline($newval)
Function: Gives the medline number
Example :
Returns : value of medline
Args : newvalue (optional)
=cut
sub medline{
my ($self,$value) = @_;
if( defined $value) {
$self->{'medline'} = $value;
}
return $self->{'medline'};
}
=head2 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)
=cut
sub pubmed {
my ($self,$value) = @_;
if( defined $value) {
$self->{'pubmed'} = $value;
}
return $self->{'pubmed'};
}
=head2 database
Title : database
Usage :
Function: Overrides DBLink database to be hard coded to 'MEDLINE', unless
the database has been set explicitely before.
Example :
Returns :
Args :
=cut
sub database{
my ($self, @args) = @_;
return $self->SUPER::database(@args) || 'MEDLINE';
}
=head2 primary_id
Title : primary_id
Usage :
Function: Overrides DBLink primary_id to provide medline number
Example :
Returns :
Args :
=cut
sub primary_id{
my ($self, @args) = @_;
return $self->medline(@args);
}
=head2 optional_id
Title : optional_id
Usage :
Function: Overrides DBLink optional_id to provide the PubMed number.
Example :
Returns :
Args :
=cut
sub optional_id{
my ($self, @args) = @_;
return $self->pubmed(@args);
}
=head2 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)
=cut
sub publisher {
my ($self,$value) = @_;
if( defined $value) {
$self->{'publisher'} = $value;
}
return $self->{'publisher'};
}
=head2 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)
=cut
sub editors {
my ($self,$value) = @_;
if( defined $value) {
$self->{'editors'} = $value;
}
return $self->{'editors'};
}
=head2 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)
=cut
sub encoded_ref {
my ($self,$value) = @_;
if( defined $value) {
$self->{'encoded_ref'} = $value;
}
return $self->{'encoded_ref'};
}
1;
]]>