Bio::SeqFeature TypedSeqFeatureI
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Summary
Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
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
ontology_termDescriptionCode
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
ontology_termdescriptionprevnextTop
sub ontology_term {
    shift->throw_not_implemented();
}

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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email - please email the BioPerl mailing list above.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _