bel_parser 1.0.0.alpha.1

data/lib/bel_parser/language/version2/functions/degradation.rb

@@ -0,0 +1,80 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      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::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member is degraded in some way such that 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
+  
+            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::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/functions/fragment.rb

@@ -0,0 +1,119 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      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::ReturnTypes::Fragment
+          DESCRIPTION = 'Denotes a protein fragment, e.g., a product of proteolytic 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
+  
+            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(
+                        value_type(
+                          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
+  
+            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(
+                        value_type(
+                          is_amino_acid_range_pattern)))),
+                  argument(
+                    parameter(
+                      prefix(
+                        any),
+                      value(
+                        value_type(
+                          encoding_of(:*))))))              
+              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

data/lib/bel_parser/language/version2/functions/from_location.rb

@@ -0,0 +1,85 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      module Functions
+        # FromLocation: Denotes the from cellular location of the abundance.
+        class FromLocation
+          extend Function
+
+          SHORT       = :fromLoc
+          LONG        = :fromLocation
+          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::FromLocation
+          DESCRIPTION = 'Denotes the from cellular location of the abundance.'.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
+  
+            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(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Location))))))              
+              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/functions/fusion.rb

@@ -0,0 +1,227 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version2
+      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::ReturnTypes::Fusion
+          DESCRIPTION = 'Specifies the abundance of a protein translated from 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
+  
+            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(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:GeneAbundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:GeneAbundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              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
+  
+            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(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:ProteinAbundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              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
+  
+            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(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:RnaAbundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:RnaAbundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              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