Method: TandemSearchTool#taxonomy_doc

Defined in:

lib/protk/tandem_search_tool.rb

#taxonomy_doc(db_info) ⇒ Object

# File 'lib/protk/tandem_search_tool.rb', line 215

def taxonomy_doc(db_info)
	throw "Invalid input db_info must be a FastaDatabase object" unless db_info.class==FastaDatabase
	database_path=db_info.path
	taxon=db_info.name
	# Parse taxonomy template file
	#
	taxo_parser=XML::Parser.file(@taxonomy_path)
	taxo_doc=taxo_parser.parse

	taxon_label=taxo_doc.find('/bioml/taxon')
	throw "Exactly one taxon label is required in the taxonomy_template file" unless taxon_label.length==1
	taxon_label[0].attributes['label']=taxon

	db_file=taxo_doc.find('/bioml/taxon/file')
	throw "Exactly one database file is required in the taxonomy_template file" unless db_file.length==1
	db_file[0].attributes['URL']=database_path

	taxo_doc
end