bel_parser 1.0.0.alpha.27-java

data/lib/bel_parser/language/version2_0/functions/products.rb

@@ -0,0 +1,79 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Products: Denotes the products of a reaction
+        class Products
+          extend Function
+
+          SHORT       = :products
+          LONG        = :products
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Products
+          DESCRIPTION = 'Denotes the products of a reaction'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.return_type
+            RETURN_TYPE
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.signatures
+            SIGNATURES
+          end
+
+          module Signatures
+            # ProductsSignature
+            class ProductsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Products))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'products(F:abundance...)products'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+          end
+
+          SIGNATURES = Signatures.constants.map do |const|
+            Signatures.const_get(const)
+          end.freeze
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb

@@ -0,0 +1,270 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # ProteinAbundance: Denotes the abundance of a protein
+        class ProteinAbundance
+          extend Function
+
+          SHORT       = :p
+          LONG        = :proteinAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ProteinAbundance
+          P_ENC       = Version2_0::ValueEncodings::ProteinAbundance
+          DESCRIPTION = 'Denotes the abundance of a protein'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.return_type
+            RETURN_TYPE
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.signatures
+            SIGNATURES
+          end
+
+          module Signatures
+            # ProteinAbundanceSignature
+            class ProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinAbundanceWithFragmentSignature
+            class ProteinAbundanceWithFragmentSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fragment))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:fragment)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinAbundanceWithFusionSignature
+            class ProteinAbundanceWithFusionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinAbundance))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(F:fusion)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinAbundanceWithLocationSignature
+            class ProteinAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:location)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinAbundanceWithProteinModificationSignature
+            class ProteinAbundanceWithProteinModificationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::ProteinModification))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:proteinModification...)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinAbundanceWithVariantSignature
+            class ProteinAbundanceWithVariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'proteinAbundance(E:proteinAbundance,F:variant)proteinAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+          end
+
+          SIGNATURES = Signatures.constants.map do |const|
+            Signatures.const_get(const)
+          end.freeze
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/functions/protein_modification.rb

@@ -0,0 +1,172 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../amino_acid'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # ProteinModification: Denotes a covalently modified protein
+        # abundance
+        class ProteinModification
+          extend Function
+
+          SHORT       = :pmod
+          LONG        = :proteinModification
+          RETURN_TYPE = Version2_0::ReturnTypes::ProteinModification
+          E_ENC       = Version2_0::ValueEncodings::ProteinModification
+          DESCRIPTION = 'Denotes a covalently modified protein
+          bundance'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.return_type
+            RETURN_TYPE
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.signatures
+            SIGNATURES
+          end
+
+          module Signatures
+            # ProteinModificationWithTypeSignature
+            class ProteinModificationWithTypeSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for modification type?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinModification))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        has_encoding,
+                        encoding_of(E_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM =
+                'proteinModification(E:modificationType)proteinModification'
+                .freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinModificationWithTypeAminoSignature
+            class ProteinModificationWithTypeAminoSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for modification type?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinModification))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        has_encoding,
+                        encoding_of(E_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        amino_acid_of(*AminoAcid.values)))))
+              end
+              private_constant :AST
+
+              STRING_FORM =
+                'proteinModification(E:modificationType,T:AminoAcid)proteinModification'
+                .freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ProteinModificationWithTypeAminoPositionSignature
+            class ProteinModificationWithTypeAminoPositionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for modification type?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ProteinModification))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        has_encoding,
+                        encoding_of(E_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        amino_acid_of(*AminoAcid.values)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))))
+              end
+              private_constant :AST
+
+              STRING_FORM =
+                'proteinModification(E:modificationType,T:AminoAcid,E:*)proteinModification'
+                .freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+          end
+
+          SIGNATURES = Signatures.constants.map do |const|
+            Signatures.const_get(const)
+          end.freeze
+        end
+      end
+    end
+  end
+end