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Summary

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

Package variables

Included modules

Inherit

Bio::SeqFeatureI

Synopsis

   # 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";
	}

    }

Description

This interface describes the extension of SeqFeatureI
to being a strongly typed SeqFeature.
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 assummed by client code as they
are scenarios where one would like to maintain the difference.

Methods

Methods description

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

Methods code

sub ontology_term {

    shift->throw_not_implemented();
}

1;

}

General documentation

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with code and data examples if at all possible.

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