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Summary

Bio::Annotation::TypeManager - Manages types for annotation collections

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

    # default type manager

    $tm = Bio::Annotation::TypeManager->new();

    # $key is a string or a Bio::Ontology::TermI compliant object
    print "The type for $key is ",$tm->type_for_key($key),"\n";

    if( !$tm->is_valid($key,$object) ) {
	$self->throw("Invalid object for key $key");
    }

Description

Manages types for annotation collections.

Methods

Methods description

 Title   : _add_type_map
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : is_valid
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : new
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : type_for_key
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

Methods code

sub _add_type_map {

   my ($self,$key,$type) = @_;
   
   $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
   $self->{'_type'}->{$key} = $type;

}

sub is_valid {

   my ($self,$key,$object) = @_;

   if( !defined $object || !ref $object ) {
       $self->throw("Cannot type an object [$object]!");
   }

   if( !$object->isa($self->type_for_key($key)) ) {
       return 0;
   } else {
       return 1;
   }

}

sub new {

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

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

   $self->{'_type'} = {};

   $self->_add_type_map('reference',"Bio::Annotation::Reference");
   $self->_add_type_map('comment',"Bio::Annotation::Comment");
   $self->_add_type_map('dblink',"Bio::Annotation::DBLink");

   return $self;

}

sub type_for_key {

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

   $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
   return $self->{'_type'}->{$key};

}

General documentation

User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.

  bioperl-l@bio.perl.org

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email birney@ebi.ac.uk
Describe contact details here

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