bel_parser 1.0.0.alpha.27-java

data/lib/bel_parser/language/version1_0/return_types/protein_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Protein abundance return type.
+        class ProteinAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ProteinAbundance
+            :proteinAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/protein_modification.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Protein modification return type.
+        class ProteinModification < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ProteinModification
+            :proteinModification
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/reactants.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Reactants return type.
+        class Reactants < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Reactants
+            :reactants
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # RibosylationActivity return type.
+        class RibosylationActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != RibosylationActivity
+            :ribosylation_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/rna_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # RNA abundance return type.
+        class RNAAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != RNAAbundance
+            :rnaAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/substitution.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Substitution return type.
+        class Substitution < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Substitution
+            :substitution
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # TransportActivity return type.
+        class TranscriptionalActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != TranscriptionalActivity
+            :transcriptional_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/transport_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # TransportActivity return type.
+        class TransportActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != TransportActivity
+            :transport_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/truncation.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Truncation return type.
+        class Truncation < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Truncation
+            :truncation
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # Abundance value encoding.
+        class Abundance < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Abundance
+            :A
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/any.rb

@@ -0,0 +1,74 @@
+require 'English'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # The Any value encoding.
+        class Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Any
+            :*
+          end
+
+          # Returns +true+ if I am a subtype of +other_return_type+; otherwise
+          # return +false+.
+          #
+          # @param  [Class]   other_return_type to compare to
+          # @return [Boolean] +true+ if I am a subtype; +false+ if not
+          def self.subtype_of?(other_return_type)
+            self <= other_return_type
+          end
+
+          # Retrieve my immediate subtypes.
+          #
+          # @return [Array<Class>] my immediate subtypes
+          def self.subtypes
+            (@subtypes ||= []).freeze
+          end
+
+          # Retrieve my transitive subtypes.
+          #
+          # @return [Array<Class>] my transitive subtypes
+          def self.transitive_subtypes
+            transitive_subtypes =
+              (@subtypes ||= []).flat_map do |subtype|
+                [subtype, subtype.subtypes]
+              end.flatten
+            transitive_subtypes << self
+            transitive_subtypes.freeze
+          end
+
+          # Inherited hook overridden to keep track of descendants. This method
+          # is inherited by all descendants.
+          #
+          # @param [Class] cls the subclass that is inheriting me
+          # @see .subtypes
+          def self.inherited(cls)
+            (@subtypes ||= []) << cls
+          end
+          private_class_method
+
+          # Raise {NotImplementedError} for +method+. Alters the exception
+          # backtrace to exclude this method.
+          #
+          # @param [#to_s] the method name
+          # @raise [NotImplementedError] for +method+
+          def self.raise_not_implemented(method)
+            msg = "#{name} must implement the #{method} method"
+            raise NotImplementedError, msg
+          rescue StandardError
+            raise(
+              $ERROR_INFO.class,
+              $ERROR_INFO.message,
+              $ERROR_INFO.backtrace[1..-1])
+          end
+          private_class_method
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/biological_process.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # BiologicalProcess value encoding.
+        class BiologicalProcess < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != BiologicalProcess
+            :B
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # ComplexAbundance value encoding.
+        class ComplexAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ComplexAbundance
+            :C
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # GeneAbundance value encoding.
+        class GeneAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != GeneAbundance
+            :G
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'rna_abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # Micro RNA abundance value encoding.
+        class MicroRNAAbundance < RNAAbundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != MicroRNAAbundance
+            :M
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/pathology.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'biological_process'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # Pathology value encoding.
+        class Pathology < BiologicalProcess
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Pathology
+            :O
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # ProteinAbundance value encoding.
+        class ProteinAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ProteinAbundance
+            :P
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb

@@ -0,0 +1,21 @@
+require_relative '../../version1_0'
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ValueEncodings
+        # RNAAbundance value encoding.
+        class RNAAbundance < Abundance
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != RNAAbundance
+            :R
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0.rb

@@ -0,0 +1,20 @@
+require_relative 'function'
+require_relative 'specification'
+require_relative 'base_specification'
+
+module BELParser
+  module Language
+    module Version2_0
+      # Version2_0 specification defines the BEL 2.0 specification.
+      class Specification < BaseSpecification
+        BaseSpecification.load_version_path('version2_0')
+
+        def initialize
+          @version = '2.0'.freeze
+          load_language_constants(Version2_0)
+          freeze
+        end
+      end
+    end
+  end
+end