bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,81 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_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::Version1_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::Version1_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/version1_0/functions/degradation.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
+        # 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::Version1_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::Version1_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/version1_0/functions/fusion.rb

@@ -0,0 +1,287 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Functions
+        # Fusion: Specifies the abundance of a protein translated from
+        # the fusion of a gene
+        class Fusion
+          extend Function
+
+          SHORT       = :fus
+          LONG        = :fusion
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Fusion
+          G_ENC       = Version1_0::ValueEncodings::GeneAbundance
+          P_ENC       = Version1_0::ValueEncodings::ProteinAbundance
+          R_ENC       = Version1_0::ValueEncodings::RNAAbundance
+          DESCRIPTION = 'Specifies the abundance of a protein translated
+          rom the fusion 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
+            # FusionGeneAbundanceWithBreakpointsSignature
+            class FusionGeneAbundanceWithBreakpointsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fusion))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(G_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:geneAbundance,E:*,E:*)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionGeneAbundanceSignature
+            class FusionGeneAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fusion))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(G_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:geneAbundance)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionProteinAbundanceWithBreakpointsSignature
+            class FusionProteinAbundanceWithBreakpointsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fusion))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:proteinAbundance,E:*,E:*)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionProteinAbundanceSignature
+            class FusionProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fusion))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:proteinAbundance)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionRNAAbundanceWithBreakpointsSignature
+            class FusionRNAAbundanceWithBreakpointsSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fusion))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(R_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(
+                        is_sequence_position))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:rnaAbundance,E:*,E:*)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionRNAAbundanceSignature
+            class FusionRNAAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Fusion))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(R_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:rnaAbundance)fusion'.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