bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,57 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates
+        # A+ -  This relationship links the abundance term in a
+        # +translocation()+ to the translocation. This relationship is
+        # direct because it is a _self_ relationship. The translocated
+        # abundance is directly acted on by the translocation
+        # process. This relationship is introduced by the BEL Compiler
+        # and may not be used by statements in BEL documents.
+        class Translocates
+          extend Relationship
+
+          SHORT       = :translocates
+          LONG        = :translocates
+          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates
+          + -  This relationship links the abundance term
+          n a +translocation()+ to the translocation. This
+          elationship is direct because it is a _self_
+          elationship. The translocated abundance
+          s directly acted on by the translocation
+          rocess. 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.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/abundance.rb

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Abundance return type.
+        class Abundance < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Abundance
+            :abundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/any.rb

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+require 'English'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # The any type.
+        class Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Any
+            :*
+          end
+
+          # Returns +true+ if I am a subtype of +other_return_type+; otherwise
+          # return +false+.
+          #
+          # @param  [Class]   other_return_type to compare to
+          # @return [Boolean] +true+ if I am a subtype; +false+ if not
+          def self.subtype_of?(other_return_type)
+            self <= other_return_type
+          end
+
+          # Retrieve my immediate subtypes.
+          #
+          # @return [Array<Class>] my immediate subtypes
+          def self.subtypes
+            (@subtypes ||= []).freeze
+          end
+
+          # Retrieve my transitive subtypes.
+          #
+          # @return [Array<Class>] my transitive subtypes
+          def self.transitive_subtypes
+            transitive_subtypes =
+              (@subtypes ||= []).flat_map do |subtype|
+                [subtype, subtype.subtypes]
+              end.flatten
+            transitive_subtypes << self
+            transitive_subtypes.freeze
+          end
+
+          # Inherited hook overridden to keep track of descendants. This method
+          # is inherited by all descendants.
+          #
+          # @param [Class] cls the subclass that is inheriting me
+          # @see .subtypes
+          def self.inherited(cls)
+            (@subtypes ||= []) << cls
+          end
+          private_class_method
+
+          # Raise {NotImplementedError} for +method+. Alters the exception
+          # backtrace to exclude this method.
+          #
+          # @param [#to_s] the method name
+          # @raise [NotImplementedError] for +method+
+          def self.raise_not_implemented(method)
+            msg = "#{name} must implement the #{method} method"
+            raise NotImplementedError, msg
+          rescue StandardError
+            raise(
+              $ERROR_INFO.class,
+              $ERROR_INFO.message,
+              $ERROR_INFO.backtrace[1..-1])
+          end
+          private_class_method
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/biological_process.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Biological process return type.
+        class BiologicalProcess < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != BiologicalProcess
+            :biologicalProcess
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # CatalyticActivity return type.
+        class CatalyticActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != CatalyticActivity
+            :catalytic_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # ChaperoneActivity return type.
+        class ChaperoneActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ChaperoneActivity
+            :chaperone_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/complex_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Complex abundance return type.
+        class ComplexAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ComplexAbundance
+            :complexAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/fusion.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Fusion return type.
+        class Fusion < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Fusion
+            :fusion
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/gene_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Gene abundance return type.
+        class GeneAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != GeneAbundance
+            :geneAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # GTP return type.
+        class GTPBoundActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != GTPBoundActivity
+            :gtp_bound_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/kinase_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # KinaseActivity return type.
+        class KinaseActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != KinaseActivity
+            :kinase_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/list.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # List return type.
+        class List < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != List
+            :list
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Micro RNA abundance return type.
+        class MicroRNAAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != MicroRNAAbundance
+            :microRNAAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/molecular_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # MolecularActivity return type.
+        class MolecularActivity < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != MolecularActivity
+            :molecular_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/pathology.rb

@@ -0,0 +1,17 @@
+require_relative 'biological_process'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Pathology return type.
+        class Pathology < BiologicalProcess
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Pathology
+            :pathology
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # PeptidaseActivity return type.
+        class PeptidaseActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != PeptidaseActivity
+            :peptidase_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb

@@ -0,0 +1,20 @@
+require_relative 'molecular_activity'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # PhosphataseActivity return type.
+        class PhosphataseActivity < MolecularActivity
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != PhosphataseActivity
+            :phosphatase_activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version1_0/return_types/products.rb

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version1_0
+      module ReturnTypes
+        # Products return type.
+        class Products < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Products
+            :products
+          end
+        end
+      end
+    end
+  end
+end