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'