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Summary

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

Package variables

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

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

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

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

Methods code

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};

}

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 _add_type_map {

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

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

1;

}

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@bioperl.org

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

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

  https://redmine.open-bio.org/projects/bioperl/

Email birney@ebi.ac.uk

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