Bio::SeqIO::game::gameSubs -- a base class for game-XML parsing Not used directly 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

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email smckay@bcgsc.bc.ca 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