bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,79 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # Reactants: Denotes the reactants of a reaction
+        class Reactants
+          extend Function
+
+          SHORT       = :reactants
+          LONG        = :reactants
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Reactants
+          DESCRIPTION = 'Denotes the reactants 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
+            # ReactantsSignature
+            class ReactantsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Reactants))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'reactants(F:abundance...)reactants'.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/version1_0/functions/reaction.rb

@@ -0,0 +1,86 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # Reaction: Denotes the frequency or abundance of events in
+        # a reaction
+        class Reaction
+          extend Function
+
+          SHORT       = :rxn
+          LONG        = :reaction
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n 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
+            # ReactionSignature
+            class ReactionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Reaction))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'reaction(F:reactants,F:products)abundance'.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/version1_0/functions/ribosylation_activity.rb

@@ -0,0 +1,114 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # RibosylationActivity: Denotes the frequency or abundance of
+        # events in which a member acts to perform post-translational
+        # modification of proteins
+        class RibosylationActivity
+          extend Function
+
+          SHORT       = :ribo
+          LONG        = :ribosylationActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::RibosylationActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events in
+          hich a member acts to perform post-translational
+          odification of proteins'.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
+            # RibosylationActivityWithComplexAbundanceSignature
+            class RibosylationActivityWithComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(RibosylationActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'ribosylationActivity(F:complexAbundance)ribosylationActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # RibosylationActivityWithProteinAbundanceSignature
+            class RibosylationActivityWithProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(RibosylationActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'ribosylationActivity(F:proteinAbundance)ribosylationActivity'.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/version1_0/functions/rna_abundance.rb

@@ -0,0 +1,122 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # RNAAbundance: Denotes the abundance of a gene
+        class RNAAbundance
+          extend Function
+
+          SHORT       = :r
+          LONG        = :rnaAbundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
+          R_ENC       = Version1_0::ValueEncodings::RNAAbundance
+          DESCRIPTION = 'Denotes the abundance of a gene'.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
+            # RNAAbundanceWithFusionSignature
+            class RNAAbundanceWithFusionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(RNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                          has_encoding,
+                          encoding_of(R_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'rnaAbundance(E:rnaAbundance,F:fusion)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # RNAAbundanceSignature
+            class RNAAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(RNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(R_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'rnaAbundance(E:rnaAbundance)geneAbundance'.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/version1_0/functions/substitution.rb

@@ -0,0 +1,93 @@
+require_relative '../../version1_0'
+require_relative '../../amino_acid'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # Substitution: Indicates the abundance of proteins with amino
+        # acid substitution sequence
+        class Substitution
+          extend Function
+
+          SHORT       = :sub
+          LONG        = :substitution
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Substitution
+          DESCRIPTION = 'Indicates the abundance of proteins with amino
+          cid substitution sequence'.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
+            # SubstitutionWithReferencePositionVariantSignature
+            class SubstitutionWithReferencePositionVariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Substitution))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        amino_acid_of(*AminoAcid.values)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        amino_acid_of(*AminoAcid.values)))))
+              end
+              private_constant :AST
+
+              STRING_FORM =
+                'substitution(T:AminoAcid,E:*,T:AminoAcid)substitution'.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