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Contents
require 'bel_parser/vendor/ast'
require 'bel_parser/parsers/ast/node'
require 'bel_parser/language/term_transformation'
module BELParser
module Language
module Version1_0
module Upgrades
class ProteinModificationTransformation
include AST::Processor::Mixin
include BELParser::Parsers::AST::Sexp
include BELParser::Language::TermTransformation
def on_term(term_node)
if ['pmod', 'proteinmodification'].include?(term_node.function.identifier.string_literal)
# straightforward replacement of first argument to pmod with pmodtype value
term_node.updated([term_node.function, update_pmod(term_node.arguments[0]), term_node.arguments[1], term_node.arguments[2] ].flatten)
else
term_node.updated([process(term_node.function), term_node.arguments.map! {|arg| process(arg)}].flatten())
end
end
def update_pmod(argument_node)
param_value = argument_node.child.value.children[0].string_literal
argument(
parameter(
prefix(
identifier('default')),
value(
identifier(PMODTYPES[param_value]))))
end
end
end
end
end
end
Version data entries
37 entries across 37 versions & 1 rubygems