Bio::SeqFeature::TypedUsereContributed PerBio::SeqFeature::TypedSeqFeatureI(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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.
perl v5.14.12011-07-Bio::SeqFeature::TypedSeqFeatureI(3)
