Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature


          # get Sequence Features in some manner, eg
          # from a Sequence object

           foreach $sf ( $seq->get_SeqFeatures() ) {
               # all sequence features must have primary_tag() return a string
               $type_as_string = $sf->primary_tag();
               if( $sf->isa("Bio::SeqFeature::TypedSeqFeatureI") ) {
                   $ot = $sf->ontology_term();
                   print "Ontology identifier:",$ot->identifier(),
                         " name:",$ot->name(),
                         " Description:",$ot->description(),"\n";

               } else {
                   print "Sequence Feature does not have an ontology type\n";



       This interface describes the extension of SeqFeatureI to being a strongly typed

       Bio::SeqFeature::TypedSeqFeatureI extends the Bio::SeqFeatureI interface (ie, a
       TypedSeqFeatureI feature must also implement all the Bio::SeqFeatureI interface as well).

       It is suggested that the primary_tag() method of SeqFeatureI return the same as the
       ontology_term()->name() of the OntologyTypedI (ie, the "string" name of the ontology type
       is used as the primary tag), but this should not be assumed by client code as they are
       scenarios where one would like to maintain the difference.


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AUTHOR - Ewan Birney

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

         Title   : ontology_term
         Usage   : my $ot = $seqfeature->ontology_term()
         Returns : a Bio::Ontology::TermI compliant object
         Args    : none
         Status  : public

       This method returns the ontology term for a strongly typed sequence feature.