NAME

       Bio::SeqIO::game::gameSubs -- a base class for game-XML parsing

SYNOPSIS

       Not used directly

DESCRIPTION

       A bag of tricks for game-XML parsing.  The PerlSAX handler methods were stolen from Chris
       Mungall's XML base class, which he stole from Ken MacLeod's XML::Handler::Subs

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

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

AUTHOR - Sheldon McKay

       Email mckays@cshl.edu

APPENDIX

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

   new
        Title   : new
        Usage   : not used directly
        Returns : a gameHandler object
        Args    : an XML filename

   go
        Title   : go
        Usage   : not used directly
        Function: starts PerlSAX XML parsing

   start_document
        Title   : start_document
        Usage   : not used directly

   end_document
        Title   : end_document
        Usage   : not used directly

   start_element
        Title   : start_element
        Usage   : not used directly

   end_element
        Title   : end_element
        Usage   : not used directly

   characters
        Title   : characters
        Usage   : not used directly

   strip_characters
        Title   : strip_characters
        Usage   : not used directly
        Function: cleans up XML element contents

   curr_element
        Title   : curr_element
        Usage   : not used directly
        Function: returns the currently open element

   flush
        Title   : flush
        Usage   : $self->flush($element) # or $element->flush
        Function: prune a branch from the XML tree
        Returns : true if successful
        Args    : an element object (optional)

   complain
        Title   : complain
        Usage   : $self->complain("This is terrible; I am not happy")
        Function: throw a non-fatal warning, formats message for pretty-printing
        Returns : nothing
        Args    : a list of strings

   dbxref
        Title   : dbxref
        Usage   : $self->db_xref($el, $tags)
        Function: an internal method to flatten dbxref elements
        Returns : the db_xref (eg wormbase:C02D5.1)
        Args    : an element object (reqd) and a hash ref of tag/values (optional)

   comment
        Title   : comment
        Usage   : $self->comment($comment_element)
        Function: a method to flatten comment elements
        Returns : a string
        Args    : an comment element (reqd) and a hash ref of tag/values (optional)
        Note    : The hope here is that we can unflatten structured comments
                  in game-derived annotations happen to make a return trip

   property
        Title   : property
        Usage   : $self->property($property_element)
        Function: an internal method to flatten property elements
        Returns : a hash reference
        Args    : an property/output element (reqd) and a hash ref of tag/values (optional)
        Note: This method is aliased to 'output' to handle structurally identical output elements

   evidence
        Title   : evidence
        Usage   : $self->evidence($evidence_element)
        Function: a method to flatten evidence elements
        Returns : a string
        Args    : an evidence element

   date
        Title   : date
        Usage   : $self->date($date_element)
        Function: a method to flatten date elements
        Returns : true if successful
        Args    : a date element

   protein_id
        Title   : protein_id
        Usage   : $pid = $self->protein_id($cds, $standard_name)
        Function: a method to search for a protein name
        Returns : a string
        Args    : the CDS object plus the transcript\'s 'standard_name'