debian man page for bio::seqfeature::typedseqfeaturei

Bio::SeqFeature::TypedSeqFeatureI(3pm)			User Contributed Perl Documentation		    Bio::SeqFeature::TypedSeqFeatureI(3pm)

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(),"
";

	       } else {
		   print "Sequence Feature does not have an ontology type
";
	       }

	   }

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.

perl v5.14.2							    2012-03-02				    Bio::SeqFeature::TypedSeqFeatureI(3pm)