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 assummed by client code as they are scenarios
where one would like to maintain the difference.
FEEDBACK¶
Mailing Lists¶
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¶
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 Bugs¶
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 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 _
ontology_term¶
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.