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#
# 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
=head1 NAME
Bio::Annotation::TypeManager - Manages types for annotation collections
=head1 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 $key");
}
=head1 DESCRIPTION
Manages types for annotation collections.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Annotation::TypeManager;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::Root);
# new() can be inherited from Bio::Root::Root
=head2 new
Title : new
Usage :
Function:
Example :
Returns :
Args :
=cut
sub new{
my ($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 $self;
}
=head2 type_for_key
Title : type_for_key
Usage :
Function:
Example :
Returns :
Args :
=cut
sub type_for_key{
my ($self,$key) = @_;
$key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
return $self->{'_type'}->{$key};
}
=head2 is_valid
Title : is_valid
Usage :
Function:
Example :
Returns :
Args :
=cut
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($key)) ) {
return 0;
} else {
return 1;
}
}
=head2 _add_type_map
Title : _add_type_map
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _add_type_map{
my ($self,$key,$type) = @_;
$key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
$self->{'_type'}->{$key} = $type;
}
1;
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