bel_parser 1.0.0.alpha.27-java

data/lib/bel_parser/language/version1_0/functions/gene_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
+        # GeneAbundance: Denotes the abundance of a gene
+        class GeneAbundance
+          extend Function
+
+          SHORT       = :g
+          LONG        = :geneAbundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
+          G_ENC       = Version1_0::ValueEncodings::GeneAbundance
+          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
+            # GeneAbundanceWithFusionSignature
+            class GeneAbundanceWithFusionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(GeneAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(G_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'geneAbundance(E:geneAbundance,F:fusion)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # GeneAbundanceSignature
+            class GeneAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(GeneAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(G_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'geneAbundance(E:geneAbundance)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/gtp_bound_activity.rb

@@ -0,0 +1,113 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # GTPBoundActivity: Denotes the frequency or abundance of events
+        # in which a member of a G-protein abundance is GTP-bound
+        class GTPBoundActivity
+          extend Function
+
+          SHORT       = :gtp
+          LONG        = :gtpBoundActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GTPBoundActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member of a G-protein abundance is
+          TP-bound'.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
+            # GTPBoundActivityOfComplexAbundanceSignature
+            class GTPBoundActivityOfComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(GTPBoundActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'gtpBoundActivity(F:complexAbundance)gtpBoundActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # GTPBoundActivityOfProteinAbundanceSignature
+            class GTPBoundActivityOfProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(GTPBoundActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'gtpBoundActivity(F:proteinAbundance)gtpBoundActivity'.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/kinase_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
+        # KinaseActivity: Denotes the frequency or abundance of events
+        # in which a member acts as a kinase, performing enzymatic
+        # phosphorylation of a substrate
+        class KinaseActivity
+          extend Function
+
+          SHORT       = :kin
+          LONG        = :kinaseActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::KinaseActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a kinase, performing
+          nzymatic phosphorylation of a substrate'.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
+            # KinaseActivityOfComplexAbundanceSignature
+            class KinaseActivityOfComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(KinaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'kinaseActivity(F:complexAbundance)kinaseActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # KinaseActivityOfProteinAbundanceSignature
+            class KinaseActivityOfProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(KinaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'kinaseActivity(F:proteinAbundance)kinaseActivity'.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/list.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
+        # List: Groups a list of terms together
+        class List
+          extend Function
+
+          SHORT       = :list
+          LONG        = :list
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::List
+          A_ENC       = Version1_0::ValueEncodings::Abundance
+          DESCRIPTION = 'Groups a list of terms together'.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
+            # ListOfAbundanceEncodingSignature
+            class ListOfAbundanceEncodingSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(List))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'list(E:abundance...)list'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ListOfAbundanceSignature
+            class ListOfAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(List))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'list(F:abundance...)list'.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