Bio::Tools::CodonTable::is_start_codon: check in case of ambiguous codons (#266)

[bioperl-live.git] / lib / Bio / Annotation / Reference.pm

#
# BioPerl module for Bio::Annotation::Reference
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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 AUTHOR - Ewan Birney 

Email birney@ebi.ac.uk

=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 strict;

use base 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, pubmed,
           start, end, consortium, rp and rg attributes


=cut

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;
}


=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 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

=cut

{
  my $DEFAULT_CB = sub { $_[0]->title || ''};

  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);
  }

}

=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;
    if (defined $self->pubmed) {
        $h->{'pubmed'} = $self->pubmed;
    }

    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


=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 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)


=cut

sub rg{
    my $self = shift;

    return $self->{'rg'} = shift if @_;
    return $self->{'rg'};
}

=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' (or 'PUBMED'
           if only pubmed id has been supplied), unless the database has been
           set explicitly before.
 Example :
 Returns :
 Args    :


=cut

sub database{
    my ($self, @args) = @_;
    my $default = 'MEDLINE';
    if (! defined $self->medline && defined $self->pubmed) {
        $default = 'PUBMED';
    }
    return $self->SUPER::database(@args) || $default;
}

=head2 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    :


=cut

sub primary_id{
    my ($self, @args) = @_;
    if (@args) {
        $self->medline(@args);
    }
    if (! defined $self->medline && defined $self->pubmed) {
        return $self->pubmed;
    }
    return $self->medline;
}

=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'};
}

=head2 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)

=cut

sub doi {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'doi'} = $value;
    }
    return $self->{'doi'};
}

=head2 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)


=cut

sub consortium{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'consortium'} = $value;
    }
    return $self->{'consortium'};
}

=head2 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)


=cut

sub gb_reference{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'gb_reference'} = $value;
    }
    return $self->{'gb_reference'};

}

1;