Provided by: libbio-perl-perl_1.7.8-1_all
NAME
Bio::Annotation::Reference - Specialised DBLink object for Literature References
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...
AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 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, pubmed, start, end, consortium, rp and rg attributes
AnnotationI implementing functions
as_text Title : as_text Usage : Function: Example : Returns : Args : display_text 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_tree Title : hash_tree Usage : Function: Example : Returns : Args : 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)
Specific accessors for References
start Title : start Usage : $self->start($newval) Function: Gives the reference start base Example : Returns : value of start Args : newvalue (optional) end Title : end Usage : $self->end($newval) Function: Gives the reference end base Example : Returns : value of end Args : newvalue (optional) 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) rg 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) 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) 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) title Title : title Usage : $self->title($newval) Function: Gives the title line (if exists) Example : Returns : value of title Args : newvalue (optional) medline Title : medline Usage : $self->medline($newval) Function: Gives the medline number Example : Returns : value of medline Args : newvalue (optional) 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) database 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_id 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_id Title : optional_id Usage : Function: Overrides DBLink optional_id to provide the PubMed number. Example : Returns : Args : 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) 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) 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) doi 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/<doi> Example : Returns : value of doi Args : newvalue (optional) consortium 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_reference 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)