bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,85 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # MicroRNAAbundance: Denotes the abundance of a processed,
+        # functional microRNA
+        class MicroRNAAbundance
+          extend Function
+
+          SHORT       = :m
+          LONG        = :microRNAAbundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MicroRNAAbundance
+          M_ENC       = Version1_0::ValueEncodings::MicroRNAAbundance
+          DESCRIPTION = 'Denotes the abundance of a processed, functional
+          icroRNA'.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
+            # MicroRNAAbundanceSignature
+            class MicroRNAAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(MicroRNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(M_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'microRNAAbundance(E:microRNAAbundance)microRNAAbundance'.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/molecular_activity.rb

@@ -0,0 +1,82 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # MolecularActivity: Denotes the frequency or abundance of events
+        # in which a member acts as a causal agent at the molecular scale
+        class MolecularActivity
+          extend Function
+
+          SHORT       = :act
+          LONG        = :molecularActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MolecularActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a causal agent at the
+          olecular scale'.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
+            # MolecularActivityOfAbundanceSignature
+            class MolecularActivityOfAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(MolecularActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'molecularActivity(F:abundance)molecularActivity'.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/pathology.rb

@@ -0,0 +1,83 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # Pathology: Denotes a disease or pathology process
+        class Pathology
+          extend Function
+
+          SHORT       = :path
+          LONG        = :pathology
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Pathology
+          O_ENC       = Version1_0::ValueEncodings::Pathology
+          DESCRIPTION = 'Denotes a disease or pathology process'.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
+            # PathologySignature
+            class PathologySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Pathology))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(O_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'pathology(E:pathology)pathology'.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/peptidase_activity.rb

@@ -0,0 +1,112 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # PeptidaseActivity: Denotes the frequency or abundance of events
+        # in which a member acts to cleave a protein
+        class PeptidaseActivity
+          extend Function
+
+          SHORT       = :pep
+          LONG        = :peptidaseActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PeptidaseActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts to cleave 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
+            # PeptidaseActivityOfComplexAbundanceSignature
+            class PeptidaseActivityOfComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(PeptidaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'peptidaseActivity(F:complexAbundance)peptidaseActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # PeptidaseActivityOfProteinAbundanceSignature
+            class PeptidaseActivityOfProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(PeptidaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'peptidaseActivity(F:proteinAbundance)peptidaseActivity'.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/phosphatase_activity.rb

@@ -0,0 +1,112 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # PhosphataseActivity: Denotes the frequency or abundance of
+        # events in which a member acts as a phosphatase
+        class PhosphataseActivity
+          extend Function
+
+          SHORT       = :phos
+          LONG        = :phosphataseActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PhosphataseActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a phosphatase'.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
+            # PhosphataseActivityOfComplexAbundanceSignature
+            class PhosphataseActivityOfComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(PhosphataseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'phosphataseActivity(F:complexAbundance)phosphataseActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # PhosphataseActivityOfProteinAbundanceSignature
+            class PhosphataseActivityOfProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(PhosphataseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'phosphataseActivity(F:proteinAbundance)phosphataseActivity'.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