plucky (3) Bio::SeqFeature::TypedSeqFeatureI.3pm.gz

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 assumed 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://github.com/bioperl/bioperl-live/issues

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.