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://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'