bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,85 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # FromLocation: Denotes the from cellular location of the
+        # abundance.
+        class FromLocation
+          extend Function
+
+          SHORT       = :fromLoc
+          LONG        = :fromLocation
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
+          L_ENC       = Version2_0::ValueEncodings::Location
+          DESCRIPTION = 'Denotes the from cellular location of the
+          bundance.'.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
+            # FromLocationSignature
+            class FromLocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(FromLocation))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(L_ENC)))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fromLocation(E:location)fromLocation'.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/fusion.rb

@@ -0,0 +1,203 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_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::Version2_0::ReturnTypes::Fusion
+          G_ENC       = Version2_0::ValueEncodings::GeneAbundance
+          P_ENC       = Version2_0::ValueEncodings::ProteinAbundance
+          R_ENC       = Version2_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
+            # FusionWithGeneEncodingSignature
+            class FusionWithGeneEncodingSignature
+              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(any))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(G_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:geneAbundance,E:*,E:geneAbundance,E:*)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionWithProteinEncodingSignature
+            class FusionWithProteinEncodingSignature
+              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(any))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(P_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:proteinAbundance,E:*,E:proteinAbundance,E:*)fusion'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # FusionWithRNAEncodingSignature
+            class FusionWithRNAEncodingSignature
+              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(any))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(R_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'fusion(E:rnaAbundance,E:*,E:rnaAbundance,E:*)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

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

@@ -0,0 +1,192 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # GeneAbundance: Denotes the abundance of a gene.
+        class GeneAbundance
+          extend Function
+
+          SHORT       = :g
+          LONG        = :geneAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
+          G_ENC       = Version2_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
+            # 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
+
+            # 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(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'geneAbundance(F:fusion)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # GeneAbundanceWithLocationSignature
+            class GeneAbundanceWithLocationSignature
+              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::Version2_0::ReturnTypes::Location))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'geneAbundance(E:abundance,F:location)geneAbundance'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+
+            # GeneAbundanceWithVariantSignature
+            class GeneAbundanceWithVariantSignature
+              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::Version2_0::ReturnTypes::Variant))))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'geneAbundance(E:geneAbundance,F:variant)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