Bio::SeqIO::game::gameSubs(3pm) 			User Contributed Perl Documentation			   Bio::SeqIO::game::gameSubs(3pm)

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

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'

perl v5.14.2							    2012-03-02					   Bio::SeqIO::game::gameSubs(3pm)