bel_parser 1.0.0.alpha.1

data/lib/bel_parser/language/version1/functions/substitution.rb

@@ -0,0 +1,96 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version1
+      module Functions
+        # Substitution: Indicates the abundance of proteins with amino acid substitution sequence
+        class Substitution
+          extend Function
+
+          SHORT       = :sub
+          LONG        = :substitution
+          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Substitution
+          DESCRIPTION = 'Indicates the abundance of proteins with amino acid substitution sequence'.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 SubstitutionWithReferencePositionVariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Substitution))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'substitution(E:*,E:*,E:*)substitution'.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/functions/transcriptional_activity.rb

@@ -0,0 +1,110 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version1
+      module Functions
+        # TranscriptionalActivity: Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes
+        class TranscriptionalActivity
+          extend Function
+
+          SHORT       = :tscript
+          LONG        = :transcriptionalActivity
+          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::TranscriptionalActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes'.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 TranscriptionalActivityOfComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(TranscriptionalActivity))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version1::ReturnTypes::ComplexAbundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'transcriptionalActivity(F:complexAbundance)transcriptionalActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class TranscriptionalActivityOfProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(TranscriptionalActivity))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'transcriptionalActivity(F:proteinAbundance)transcriptionalActivity'.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/functions/translocation.rb

@@ -0,0 +1,100 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version1
+      module Functions
+        # Translocation: Denotes the frequency or abundance of events in which members move between locations
+        class Translocation
+          extend Function
+
+          SHORT       = :tloc
+          LONG        = :translocation
+          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which members move between locations'.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 TranslocationSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Translocation))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Abundance))))),
+                argument(
+                  parameter(
+                    prefix(
+                      identifier(
+                        has_namespace,
+                        namespace_of(:*))),
+                    value(
+                      value_type(
+                        has_encoding,
+                        encoding_of(:Abundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'translocation(F:abundance,E:abundance,E: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/functions/transport_activity.rb

@@ -0,0 +1,110 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version1
+      module Functions
+        # TransportActivity: Denotes the frequency or abundance of events in which a member directs acts to enable the directed movement of substances into, out of, within, or between cells
+        class TransportActivity
+          extend Function
+
+          SHORT       = :tport
+          LONG        = :transportActivity
+          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::TransportActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member directs acts to enable the directed movement of substances into, out of, within, or between 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
+  
+            class TransportActivityOfComplexAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(TransportActivity))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version1::ReturnTypes::ComplexAbundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'transportActivity(F:complexAbundance)transportActivity'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+  
+            class TransportActivityOfProteinAbundanceSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(TransportActivity))),
+                argument(
+                  term(
+                    function(
+                      identifier(
+                        return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'transportActivity(F:proteinAbundance)transportActivity'.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/functions/truncation.rb

@@ -0,0 +1,82 @@
+require_relative '../../version1'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantic_ast'
+
+module BELParser
+  module Language
+    module Version1
+      module Functions
+        # Truncation: Indicates an abundance of proteins with truncation sequence variants
+        class Truncation
+          extend Function
+
+          SHORT       = :trunc
+          LONG        = :truncation
+          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Truncation
+          DESCRIPTION = 'Indicates an abundance of proteins with truncation sequence variants'.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 TruncationWithPositionSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                function(
+                  identifier(
+                    function_of(Truncation))),
+                argument(
+                  parameter(
+                    prefix(
+                      any),
+                    value(
+                      value_type(
+                        encoding_of(:*))))))              
+              end
+              private_constant :AST
+
+              STRING_FORM = 'truncation(E:*)truncation'.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