NAME

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

SYNOPSIS

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

DESCRIPTION

       Class to map $seq_feature->primary_tag

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 lists  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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chris Mungall

       Email:  cjm@fruitfly.org

APPENDIX

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

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

   set_ParentIDs_from_hierarchy()
        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

   create_hierarchy_from_ParentIDs
        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    :

   generate_unique_persistent_id
        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

         seq_id
         primary_tag
         start
         end

       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