/ 
bioperl-1.5.2_004-RCd
/ Bio::SeqIO::game::gameSubs

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

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'