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 listsSupport
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 filenamego
Title : go
Usage : not used directly
Function: starts PerlSAX XML parsingstart_document
Title : start_document
Usage : not used directly end_document
Title : end_document
Usage : not used directlystart_element
Title : start_element
Usage : not used directlyend_element
Title : end_element
Usage : not used directlycharacters
Title : characters
Usage : not used directlystrip_characters
Title : strip_characters
Usage : not used directly
Function: cleans up XML element contentscurr_element
Title : curr_element
Usage : not used directly
Function: returns the currently open elementflush
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 stringsdbxref
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 tripproperty
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 elementsevidence
Title : evidence
Usage : $self->evidence($evidence_element)
Function: a method to flatten evidence elements
Returns : a string
Args : an evidence elementdate
Title : date
Usage : $self->date($date_element)
Function: a method to flatten date elements
Returns : true if successful
Args : a date elementprotein_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'