bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,190 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # ComplexAbundance: Denotes the abundance of a molecular complex.
+        class ComplexAbundance
+          extend Function
+
+          SHORT       = :complex
+          LONG        = :complexAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ComplexAbundance
+          C_ENC       = Version2_0::ValueEncodings::ComplexAbundance
+          DESCRIPTION = 'Denotes the abundance of a molecular
+          omplex.'.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
+            # NamedComplexAbundanceSignature
+            class NamedComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(C_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(E:abundance)complexAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # NamedComplexAbundanceWithLocationSignature
+            class NamedComplexAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(C_ENC)))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(E:abundance,F:location)complexAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ComposedComplexAbundanceSignature
+            class ComposedComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(F:abundance...)complexAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # ComposedComplexAbundanceWithLocationSignature
+            class ComposedComplexAbundanceWithLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'complexAbundance(F:abundance...,F:location)complexAbundance'.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/composite_abundance.rb

@@ -0,0 +1,81 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # CompositeAbundance: Denotes the frequency or abundance of
+        # events in which members are present.
+        class CompositeAbundance
+          extend Function
+
+          SHORT       = :composite
+          LONG        = :compositeAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which members are present.'.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
+            # CompositeAbundanceSignature
+            class CompositeAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(CompositeAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'compositeAbundance(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/degradation.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
+        # Degradation: Denotes the frequency or abundance of events
+        # in which a member is degraded in some way such that it is no
+        # longer a member.
+        class Degradation
+          extend Function
+
+          SHORT       = :deg
+          LONG        = :degradation
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member is degraded in some way such
+          hat it is no longer a member.'.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
+            # DegradationSignature
+            class DegradationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Degradation))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'degradation(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/fragment.rb

@@ -0,0 +1,116 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Fragment: Denotes a protein fragment, e.g., a product of
+        # proteolytic cleavage.
+        class Fragment
+          extend Function
+
+          SHORT       = :frag
+          LONG        = :fragment
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fragment
+          DESCRIPTION = 'Denotes a protein fragment, e.g., a product of
+          roteolytic cleavage.'.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
+            # FragmentWithRangeSignature
+            class FragmentWithRangeSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fragment))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_amino_acid_range_pattern))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fragment(E:aminoAcidRange)abundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FragmentWithRangeDescriptorSignature
+            class FragmentWithRangeDescriptorSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fragment))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_amino_acid_range_pattern))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fragment(E:aminoAcidRange,E:*)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