Class: BEL::Model::Term

Inherits:
Object
  • Object
show all
Includes:
Comparable
Defined in:
lib/bel/evidence_model/bel_term.rb,
lib/bel/extensions/rdf/rdf.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fx, *arguments) ⇒ Term

Returns a new instance of Term.



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# File 'lib/bel/evidence_model/bel_term.rb', line 7

def initialize(fx, *arguments)
  @fx = fx
  @arguments = (arguments ||= []).flatten
end

Instance Attribute Details

#arguments ⇒ Object

Returns the value of attribute arguments.



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# File 'lib/bel/evidence_model/bel_term.rb', line 5

def arguments
  @arguments
end

#fx ⇒ Object

Returns the value of attribute fx.



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# File 'lib/bel/evidence_model/bel_term.rb', line 5

def fx
  @fx
end

#signature ⇒ Object

Returns the value of attribute signature.



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# File 'lib/bel/evidence_model/bel_term.rb', line 5

def signature
  @signature
end

Instance Method Details

#<<(item) ⇒ Object 



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# File 'lib/bel/evidence_model/bel_term.rb', line 38

def <<(item)
  @arguments << item
end

#==(other) ⇒ Object Also known as: eql? 



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# File 'lib/bel/evidence_model/bel_term.rb', line 66

def ==(other)
  return false if other == nil
  @fx == other.fx && @arguments == other.arguments
end

#hash ⇒ Object 



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# File 'lib/bel/evidence_model/bel_term.rb', line 62

def hash
  [@fx, @arguments].hash
end

#invalid_signatures ⇒ Object 



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# File 'lib/bel/evidence_model/bel_term.rb', line 58

def invalid_signatures
  @fx.signatures.find_all { |sig| (@signature <=> sig) < 0 }
end

#rdf_type ⇒ Object 



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# File 'lib/bel/extensions/rdf/rdf.rb', line 74

def rdf_type
  if respond_to? 'fx'
    fx = @fx.respond_to?(:short_form) ? @fx.short_form : @fx.to_s.to_sym
    if [:p, :proteinAbundance].include?(fx) &&
       @arguments.find{ |x|
         if x.is_a? BEL::Model::Term
           arg_fx = x.fx
           arg_fx = arg_fx.respond_to?(:short_form) ? arg_fx.short_form : arg_fx.to_s.to_sym
           [:pmod, :proteinModification].include?(arg_fx)
         else
           false
         end
       }

      return BEL::RDF::BELV.ModifiedProteinAbundance
    end

    if [:p, :proteinAbundance].include?(fx) &&
       @arguments.find{ |x|
         if x.is_a? BEL::Model::Term
           arg_fx = x.fx
           arg_fx = arg_fx.respond_to?(:short_form) ? arg_fx.short_form : arg_fx.to_s.to_sym
           BEL::RDF::PROTEIN_VARIANT.include?(arg_fx)
         else
           false
         end
       }

      return BEL::RDF::BELV.ProteinVariantAbundance
    end

    BEL::RDF::FUNCTION_TYPE[fx] || BEL::RDF::BELV.Abundance
  end
end

#to_bel ⇒ Object Also known as: to_s 



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# File 'lib/bel/evidence_model/bel_term.rb', line 72

def to_bel
  arguments = [@arguments].flatten.map(&:to_bel).join(',') 
  "#{@fx.short_form}(#{arguments})"
end

#to_rdf ⇒ Object 



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# File 'lib/bel/extensions/rdf/rdf.rb', line 109

def to_rdf
  uri = to_uri
  statements = []

  # rdf:type
  type = rdf_type
  statements << [uri, BEL::RDF::RDF.type, BEL::RDF::BELV.Term]
  statements << [uri, BEL::RDF::RDF.type, type]
  fx = @fx.respond_to?(:short_form) ? @fx.short_form : @fx.to_s.to_sym
  if BEL::RDF::ACTIVITY_TYPE.include? fx
    statements << [uri, BEL::RDF::BELV.hasActivityType, BEL::RDF::ACTIVITY_TYPE[fx]]
  end

  # rdfs:label
  statements << [uri, BEL::RDF::RDFS.label, to_s.force_encoding('UTF-8')]

  # special proteins (does not recurse into pmod)
  if [:p, :proteinAbundance].include?(fx)
    pmod =
      @arguments.find{ |x|
        if x.is_a? BEL::Model::Term
          arg_fx = x.fx
          arg_fx = arg_fx.respond_to?(:short_form) ? arg_fx.short_form : arg_fx.to_s.to_sym
          [:pmod, :proteinModification].include?(arg_fx)
        else
          false
        end
      }
    if pmod
      mod_string = pmod.arguments.map(&:to_s).join(',')
      mod_type = BEL::RDF::MODIFICATION_TYPE.find {|k,v| mod_string.start_with? k}
      mod_type = (mod_type ? mod_type[1] : BEL::RDF::BELV.Modification)
      statements << [uri, BEL::RDF::BELV.hasModificationType, mod_type]
      last = pmod.arguments.last.to_s
      if last.match(/^\d+$/)
        statements << [uri, BEL::RDF::BELV.hasModificationPosition, last.to_i]
      end
      # link root protein abundance as hasChild
      root_param = @arguments.find{|x| x.is_a? BEL::Model::Parameter}
      (root_id, root_statements) = BEL::Model::Term.new(:p, [root_param]).to_rdf
      statements << [uri, BEL::RDF::BELV.hasChild, root_id]
      statements += root_statements
      return [uri, statements]
    elsif @arguments.find{|x| x.is_a? BEL::Model::Term and BEL::RDF::PROTEIN_VARIANT.include? x.fx}
      # link root protein abundance as hasChild
      root_param = @arguments.find{|x| x.is_a? BEL::Model::Parameter}
      (root_id, root_statements) = BEL::Model::Term.new(:p, [root_param]).to_rdf
      statements << [uri, BEL::RDF::BELV.hasChild, root_id]
      statements += root_statements
      return [uri, statements]
    end
  end

  # BEL::RDF::BELV.hasConcept]
  @arguments.find_all{ |x|
    x.is_a? BEL::Model::Parameter and x.ns != nil
  }.each do |param|
    concept_uri = param.ns.to_rdf_vocabulary[param.value.to_s]
    statements << [uri, BEL::RDF::BELV.hasConcept, BEL::RDF::RDF::URI(Addressable::URI.encode(concept_uri))]
  end

  # BEL::RDF::BELV.hasChild]
  @arguments.find_all{|x| x.is_a? BEL::Model::Term}.each do |child|
    (child_id, child_statements) = child.to_rdf
    statements << [uri, BEL::RDF::BELV.hasChild, child_id]
    statements += child_statements
  end

  return [uri, statements]
end

#to_uri ⇒ Object 



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# File 'lib/bel/extensions/rdf/rdf.rb', line 69

def to_uri
  tid = to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
  BEL::RDF::BELR[URI::encode(tid)]
end

#valid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bel/evidence_model/bel_term.rb', line 42

def valid?
  invalid_signatures = @arguments.find_all { |arg|
    arg.is_a? Term
  }.find_all { |term|
    not term.valid?
  }
  return false if not invalid_signatures.empty?

  sigs = @fx.signatures
  sigs.any? do |sig| (@signature <=> sig) >= 0 end
end

#valid_signatures ⇒ Object 



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# File 'lib/bel/evidence_model/bel_term.rb', line 54

def valid_signatures
  @fx.signatures.find_all { |sig| (@signature <=> sig) >= 0 }
end