Bio::SeqFeature TypedSeqFeatureI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
Package variables
No package variables defined.
Included modules
   # 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 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 description
ontology_termcode    nextTop
  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.
Methods code
sub ontology_term {

General documentation
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AUTHOR - Ewan BirneyTop
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