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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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    # 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

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Manages types for annotation collections.

FEEDBACK

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Mailing Lists

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

Support

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.

Reporting Bugs

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/

AUTHOR - Ewan Birney

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Email birney@ebi.ac.uk

APPENDIX

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

new

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

type_for_key

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

is_valid

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

_add_type_map

 Title   : _add_type_map
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Annotation::TypeManager
#
# 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



# Let the code begin...


package Bio::Annotation::TypeManager;
use strict;

# Object preamble - inherits from Bio::Root::Root



use base qw(Bio::Root::Root);
# new() can be inherited from Bio::Root::Root


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;