bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,161 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Abundance: Denotes the abundance of an entity.
+        class Abundance
+          extend Function
+
+          SHORT       = :a
+          LONG        = :abundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
+          A_ENC       = Version2_0::ValueEncodings::Abundance
+          DESCRIPTION = 'Denotes the abundance of an entity.'.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
+            # AbundanceSignature
+            class AbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'abundance(E:abundance)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # AbundanceWithLocationSignature
+            class AbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'abundance(E:abundance,F:location)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # AbundanceWithMolecularActivitySignature
+            class AbundanceWithMolecularActivitySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'abundance(E:abundance, F:molecularActivity)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/version2_0/functions/activity.rb

@@ -0,0 +1,118 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Activity: Denotes the frequency or abundance of events in
+        # which a member acts as a causal agent at the molecular scale.
+        class Activity
+          extend BELParser::Language::Function
+
+          SHORT       = :act
+          LONG        = :activity
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Activity
+          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
+            # ActivitySignature
+            class ActivitySignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Activity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'activity(F:abundance)activity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ActivityWithSpecificActivityTypeSignature
+            class ActivityWithSpecificActivityTypeSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Activity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'activity(F:abundance, F:molecularActivity)activity'.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/biological_process.rb

@@ -0,0 +1,84 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # BiologicalProcess: Denotes a process or population of events.
+        class BiologicalProcess
+          extend Function
+
+          SHORT       = :bp
+          LONG        = :biologicalProcess
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::BiologicalProcess
+          B_ENC       = Version2_0::ValueEncodings::BiologicalProcess
+          DESCRIPTION = 'Denotes a process or population of
+          vents.'.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
+            # BiologicalProcessSignature
+            class BiologicalProcessSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(BiologicalProcess))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(B_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'biologicalProcess(E:biologicalProcess)biologicalProcess'.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/cell_secretion.rb

@@ -0,0 +1,83 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # CellSecretion: Denotes the frequency or abundance of events
+        # in which members of an abundance move from cells to regions
+        # outside of the cells.
+        class CellSecretion
+          extend Function
+
+          SHORT       = :sec
+          LONG        = :cellSecretion
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which members of an abundance move from cells
+          o regions outside of the cells.'.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
+            # CellSecretionSignature
+            class CellSecretionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(CellSecretion))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'cellSecretion(F:abundance)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/version2_0/functions/cell_surface_expression.rb

@@ -0,0 +1,83 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # CellSurfaceExpression: Denotes the frequency or abundance of
+        # events in which members of an abundance move to the surface
+        # of cells.
+        class CellSurfaceExpression
+          extend Function
+
+          SHORT       = :surf
+          LONG        = :cellSurfaceExpression
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in
+          hich members of an abundance move to the surface
+          f cells.'.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
+            # CellSurfaceExpressionSignature
+            class CellSurfaceExpressionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(CellSurfaceExpression))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'cellSurfaceExpression(F:abundance)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