Class: BELParser::Language::Version1_0::Upgrades::FusionTransformation

Inherits:
Object
  • Object
show all
Includes:
AST::Processor::Mixin, TermTransformation, Parsers::AST::Sexp
Defined in:
lib/bel_parser/language/version1_0/upgrades/fusion_transformation.rb

Constant Summary

Constants included from TermTransformation

TermTransformation::ACTIVITIES, TermTransformation::PMODTYPES

Instance Method Summary collapse

Methods included from TermTransformation

#collapse, #on_argument, #on_function, #on_nested_statement, #on_object, #on_observed_term, #on_simple_statement, #on_statement, #on_subject

Methods included from Parsers::AST::Sexp

#annotation_definition, #argument, #blank_line, build, #comment, #comment_line, #document_property, #domain, #function, #identifier, #keyword, #list, #list_item, #multi_identifier, #name, #namespace_definition, #nested_statement, #object, #observed_term, #parameter, #pattern, #prefix, #relationship, #set, #simple_statement, #statement, #string, #subject, #term, #unset, #uri, #url, #value

Methods included from AST::Processor::Mixin

#handler_missing, #process, #process_all

Instance Method Details

#fusion_node?(term_node) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bel_parser/language/version1_0/upgrades/fusion_transformation.rb', line 14

def fusion_node?(term_node)
  fusion_func = false

  fusionable_func =
    [
      'p', 'proteinAbundance',
      'r', 'rnaAbundance',
      'g', 'geneAbundance'
    ].include?(term_node.function.identifier.string_literal)
  return false unless fusionable_func

  if term_node.arguments[1] && term_node.arguments[1].child.respond_to?('function')
      ['fus', 'fusion'].include?(term_node.arguments[1].child.function.identifier.string_literal)
  else
    false
  end
end

#on_term(term_node) ⇒ Object 



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# File 'lib/bel_parser/language/version1_0/upgrades/fusion_transformation.rb', line 32

def on_term(term_node)
  if fusion_node?(term_node)
    fusionable_func = term_node.function.identifier.string_literal
    parameter = term_node.arguments[0].child

    first_prefix = parameter.prefix.identifier.string_literal
    first_value = parameter.value.children[0].string_literal
    parameter = term_node.arguments[1].child.arguments[0].child
    second_prefix = parameter.prefix.identifier.string_literal
    second_value = parameter.value.children[0].string_literal

    term(
      function(
        identifier(fusionable_func)),
        term(
          function(
            identifier('fus')),
          argument(
            parameter(
              prefix(
                identifier(first_prefix)),
              value(
                identifier(first_value)))),
          argument(
            parameter(
              prefix(
                identifier(second_prefix)),
              value(
                  identifier(second_value))))))
  else
    term_node.updated([process(term_node.function), term_node.arguments.map! {|arg| process(arg)}].flatten())
  end
end