Bio::Annotation TypeManager
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Annotation::TypeManager - Manages types for annotation collections
Package variables
No package variables defined.
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 $key"); }
Description
Manages types for annotation collections.
Methods
newDescriptionCode
type_for_keyDescriptionCode
is_validDescriptionCode
_add_type_mapDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage :
Function:
Example :
Returns :
Args :
type_for_keycodeprevnextTop
 Title   : type_for_key
Usage :
Function:
Example :
Returns :
Args :
is_validcodeprevnextTop
 Title   : is_valid
Usage :
Function:
Example :
Returns :
Args :
_add_type_mapcodeprevnextTop
 Title   : _add_type_map
Usage :
Function:
Example :
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
   my ($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 $self;
}
type_for_keydescriptionprevnextTop
sub type_for_key {
   my ($self,$key) = @_;

   $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI");
   return $self->{'_type'}->{$key};
}
is_validdescriptionprevnextTop
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($key)) ) {
       return 0;
   } else {
       return 1;
   }
}
_add_type_mapdescriptionprevnextTop
sub _add_type_map {
   my ($self,$key,$type) = @_;

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

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _