Raw content of Bio::Annotation::Reference # $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;