Summary

Bio::Annotation::DBLink - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::AnnotationI Bio::Root::Root

Synopsis

   $link1 = new Bio::Annotation::DBLink(-database => 'TSC',
                                        -primary_id => 'TSC0000030'
					);

   #or 

   $link2 = new Bio::Annotation::DBLink();
   $link2->database('dbSNP');
   $link2->primary_id('2367');

   # $feat is Bio::Annotation object, Bio::SeqFeature::Generic inherits it
   $feat->add_DBLink($link2);

Description

Provides an object which represents a link from one onbject to something
in another database without proscribing what is in the other database

Methods

Methods description

 Title   : as_text
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : hash_tree
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : database
 Usage   : $self->database($newval)
 Function: set/get on the database string. Databases are just
           a string here which can then be interpretted elsewhere
 Example : 
 Returns : value of database
 Args    : newvalue (optional)

 Title   : primary_id
 Usage   : $self->primary_id($newval)
 Function: set/get on the primary id (a string)
           The primary id is the main identifier used for this object in 
           the database. Good examples would be accession numbers. The id
           is meant to be the main, stable identifier for this object
 Example : 
 Returns : value of primary_id
 Args    : newvalue (optional)

 Title   : optional_id
 Usage   : $self->optional_id($newval)
 Function: get/set for the optional_id (a string)
           optional id is a slot for people to use as they wish. The main
           issue is that some databases do not have a clean single string
           identifier scheme. It is hoped that the primary_id can behave like
           a reasonably sane "single string identifier" of objects, and people
           can use/abuse optional ids to their heart's content to provide
           precise mappings. 
 Example : 
 Returns : value of optional_id
 Args    : newvalue (optional)

 Title   : comment
 Usage   : $self->comment($newval)
 Function: get/set of comments (comment object)
           Sets or gets comments of this dblink, which is sometimes relevant
 Example : 
 Returns : value of comment (Bio::Annotation::Comment)
 Args    : newvalue (optional)

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  my ($database, $primary_id, $optional_id, $comment) =
      $self->_rearrange([qw(DATABASE
			    PRIMARY_ID
			    OPTIONAL_ID
			    COMMENT
			    )], @args);
  
  $database    && $self->database($database);
  $primary_id  && $self->primary_id($primary_id);
  $optional_id && $self->optional_id($optional_id);
  $comment     && $self->comment($comment);
  
  return $self;

}

sub as_text {

   my ($self) = @_;

   return "Direct database link to ".$self->primary_id." in database ".$self->database;

}

sub hash_tree {

   my ($self) = @_;
   
   my $h = {};
   $h->{'database'}   = $self->database;
   $h->{'primary_id'} = $self->primary_id;
   if( defined $self->optional_id ) {
       $h->{'optional_id'} = $self->optional_id;
   }
   if( defined $self->comment ) {
       # we know that comments have hash_tree methods
       $h->{'comment'} = $self->comment;
   }

   return $h;

}

sub database {

   my ($self,$value) = @_;

   if( defined $value) {
      $self->{'database'} = $value;
    }
    return $self->{'database'};

}

sub primary_id {

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

}

sub optional_id {

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

}

sub comment {

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

}

General documentation

Ewan Birney - birney@ebi.ac.uk

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _