bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,114 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      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_0::ReturnTypes::TranscriptionalActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member directly acts to control
+          ranscription 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
+            # TranscriptionalActivityOfComplexAbundanceSignature
+            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_0::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
+
+            # TranscriptionalActivityOfProteinAbundanceSignature
+            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_0::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_0/functions/translocation.rb

@@ -0,0 +1,98 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      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_0::ReturnTypes::Abundance
+          A_ENC       = Version1_0::ValueEncodings::Abundance
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n 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
+            # TranslocationSignature
+            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_0::ReturnTypes::Abundance))))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))),
+                  argument(
+                    parameter(
+                      prefix(
+                        has_namespace,
+                        namespace_of(:*)),
+                      value(
+                        has_encoding,
+                        encoding_of(A_ENC)))))
+              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_0/functions/transport_activity.rb

@@ -0,0 +1,115 @@
+require_relative '../../version1_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version1_0
+      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_0::ReturnTypes::TransportActivity
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member directs acts to enable the
+          irected movement of substances into, out of,
+          ithin, 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
+            # TransportActivityOfComplexAbundanceSignature
+            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_0::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
+
+            # TransportActivityOfProteinAbundanceSignature
+            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_0::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_0/functions/truncation.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
+        # Truncation: Indicates an abundance of proteins with truncation
+        # sequence variants
+        class Truncation
+          extend Function
+
+          SHORT       = :trunc
+          LONG        = :truncation
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Truncation
+          DESCRIPTION = 'Indicates an abundance of proteins with
+          runcation 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
+            # TruncationWithPositionSignature
+            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(
+                        is_sequence_position))))
+              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

data/lib/bel_parser/language/version1_0/relationships/acts_in.rb

@@ -0,0 +1,61 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # ActsIn:  +A actsIn f(A)+ -  This relationship links
+        # an abundance term to the activity term for the same
+        # abundance. This relationship is direct because it is a _self_
+        # relationship, the abundance acts in its own activity. For
+        # protein abundance p(A) and its molecular activity kin(p(A),
+        # +p(A) actsIn kin(p(A))+. This relationship is introduced by the
+        # BEL Compiler and may not be used by statements in BEL documents.
+        class ActsIn
+          extend Relationship
+
+          SHORT       = :actsIn
+          LONG        = :actsIn
+          DESCRIPTION = ' +A actsIn f(A)+ -  This relationship links an
+          bundance term to the activity term for the same
+          bundance. This relationship is direct because
+          t is a _self_ relationship, the abundance acts
+          n its own activity. For protein abundance p(A)
+          nd its molecular activity kin(p(A), +p(A) actsIn
+          in(p(A))+. This relationship is introduced by the
+          EL Compiler and may not be used by statements in
+          EL documents.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
+        end
+      end
+    end
+  end
+end