Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::SeqFeature::Tools::IDHandler - maps $seq_feature->primary_tag


         use Bio::SeqIO;
         use Bio::SeqFeature::Tools::IDHandler;


       Class to map $seq_feature->primary_tag


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AUTHOR - Chris Mungall



       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::IDHandler->new();
        Function: constructor
        Example :
        Returns : a new Bio::SeqFeature::Tools::IDHandler
        Args    : see below

        Title   : set_ParentIDs_from_hierarchy()
        Usage   : $idhandler->set_ParentIDs_from_hierarchy($fholder)
        Function: populates tags Parent and ID via holder hierarchy
        Example :
        Returns :
        Args    : Bio::featureHolderI (either a SeqFeature or a Seq)

       This is mainly for GFF3 export

       GFF3 uses the tags ID and Parent to represent the feature containment hierarchy; it does
       NOT use the feature holder tree

       This method sets Parent (and ID for any parents not set) based on feature
       holder/containement hierarchy, ready for GFF3 output

        Title   : create_hierarchy_from_ParentIDs
        Usage   : $idhandler->set_ParentIDs_from_hierarchy($fholder)
        Function: inverse of set_ParentIDs_from_hierarchy
        Example :
        Returns : list of top SeqFeatures
        Args    :

        Title   : generate_unique_persistent_id
        Usage   :
        Function: generates a unique and persistent identifier for this
        Example :
        Returns : value of primary_id (a scalar)
        Args    :

       Will generate an ID, and set primary_id() (see above)

       The ID is a string generated from


       There are three underlying assumptions: that all the above accessors are set; that seq_id
       is a persistent and unique identifier for the sequence containing this feature; and that

         (seq_id, primary_tag, start, end)

       is a "unique constraint" over features

       The ID is persistent, so long as none of these values change - if they do, it is
       considered a separate entity