Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features


         use Bio::SeqIO;
         use Bio::SeqFeature::Tools::FeatureNamer;

         # first fetch a genbank SeqI object
         $seqio =
         $seq = $seqio->next_seq();

         $namer = Bio::SeqFeature::Tools::FeatureNamer->new;
         my @features = $seq->get_SeqFeatures;
         foreach my $feature (@features) {
           $namer->name_feature($feature) unless $feature->display_name;


       This is a helper class for providing names for SeqFeatures

       The Bio::SeqFeatureI class provides a display_name method. Typically the display_name is
       not set when parsing formats such as genbank - instead properties such as label, product
       or gene are set in a somewhat inconsistent manner.

       In addition, when generating subfeatures (for example, exons that are subfeatures of a
       transcript feature), it is often desirable to name these subfeatures before either
       exporting to another format or reporting to the user.

       This module is intended to help given uniform display_names to features and their


       Currently the naming policy is hardcoded. It may be desirable to allow plugging in
       variations on naming policies; this could be done either by subclassing, anonymous
       subroutines (closures) or parameterization. Contact the author if you feel you have need
       for a different naming policy


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AUTHOR - Chris Mungall

       Email:  cjm AT fruitfly DOT org


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new();
        Function: constructor
        Example :
        Returns : a new Bio::SeqFeature::Tools::FeatureNamer
        Args    : see below

        Title   : name_feature
        Usage   : $namer->name_feature($sf);
        Function: sets display_name
        Example :
        Returns :
        Args    : L<Bio::SeqFeatureI>

       This method calls generate_feature_name() and uses the returned value to set the
       display_name of the feature

        Title   : name_contained_features
        Usage   : $namer->name_contained_features($sf);
        Function: sets display_name for all features contained by sf
        Example :
        Returns :
        Args    : L<Bio::SeqFeatureI>

       iterates through all subfeatures of a certain feature (using get_all_SeqFeatures) and
       names each subfeatures, based on the generated name for the holder feature

       A subfeature is named by concatenating the generated name of the container feature with
       the type and a number.

       For example, if the containing feature is a gene with display name dpp, subfeatures will
       be named dpp-mRNA-1 dpp-mRNA2 dpp-exon1 dpp-exon2 etc

        Title   : generate_feature_name
        Usage   : $name = $namer->generate_feature_name($sf);
        Function: derives a sensible human readable name for a $sf
        Example :
        Returns : str
        Args    : L<Bio::SeqFeatureI>

       returns a generated name (but does not actually set display_name).

       If display_name is already set, the method will return this

       Otherwise, the name will depend on the property:


       (in order of priority)