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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:

   http://bugzilla.open-bio.org/
 
 

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'