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
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)
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'