NAME¶

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

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 assumed by client code as they are scenarios where one would like to maintain the difference.

FEEDBACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney¶

Email - please email the BioPerl mailing list above.

APPENDIX¶

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