bel_parser 1.0.0.alpha.7 → 1.0.0.alpha.8

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

@@ -14,7 +14,8 @@ module BELParser
           SHORT       = :complex
           LONG        = :complexAbundance
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ComplexAbundance
-          DESCRIPTION = 'Denotes the abundance of a molecular complex.'.freeze
+          DESCRIPTION = 'Denotes the abundance of a molecular
+          omplex.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +38,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # NamedComplexAbundanceSignature
             class NamedComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +46,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ComplexAbundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))))
               end
               private_constant :AST
 
@@ -72,7 +73,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # NamedComplexAbundanceWithLocationSignature
             class NamedComplexAbundanceWithLocationSignature
               extend BELParser::Language::Signature
 
@@ -80,24 +82,24 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ComplexAbundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))              
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
 
@@ -112,7 +114,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # ComposedComplexAbundanceSignature
             class ComposedComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -120,14 +123,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ComplexAbundance))),
-                variadic_arguments(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -142,7 +145,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # ComposedComplexAbundanceWithLocationSignature
             class ComposedComplexAbundanceWithLocationSignature
               extend BELParser::Language::Signature
 
@@ -150,19 +154,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(ComplexAbundance))),
-                variadic_arguments(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))              
+                  function(
+                    identifier(
+                      function_of(ComplexAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
 
@@ -177,7 +181,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version2_0
       module Functions
-        # CompositeAbundance: Denotes the frequency or abundance of events in which members are present.
+        # CompositeAbundance: Denotes the frequency or abundance of
+        # events in which members are present.
         class CompositeAbundance
           extend Function
 
           SHORT       = :composite
           LONG        = :compositeAbundance
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which members are present.'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which members are present.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # CompositeAbundanceSignature
             class CompositeAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +47,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CompositeAbundance))),
-                variadic_arguments(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(CompositeAbundance))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +69,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version2_0
       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.
+        # 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_0::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
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member is degraded in some way such
+          hat it is no longer a member.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # DegradationSignature
             class DegradationSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Degradation))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(Degradation))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version2_0
       module Functions
-        # Fragment: Denotes a protein fragment, e.g., a product of proteolytic cleavage.
+        # 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_0::ReturnTypes::Fragment
-          DESCRIPTION = 'Denotes a protein fragment, e.g., a product of proteolytic cleavage.'.freeze
+          DESCRIPTION = 'Denotes a protein fragment, e.g., a product of
+          roteolytic cleavage.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # FragmentWithRangeSignature
             class FragmentWithRangeSignature
               extend BELParser::Language::Signature
 
@@ -68,7 +70,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # FragmentWithRangeDescriptorSignature
             class FragmentWithRangeDescriptorSignature
               extend BELParser::Language::Signature
 
@@ -91,7 +94,7 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))              
+                          encoding_of(:*))))))
               end
               private_constant :AST
 
@@ -106,7 +109,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version2_0
       module Functions
-        # FromLocation: Denotes the from cellular location of the abundance.
+        # 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
-          DESCRIPTION = 'Denotes the from cellular location of the abundance.'.freeze
+          DESCRIPTION = 'Denotes the from cellular location of the
+          bundance.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # FromLocationSignature
             class FromLocationSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +47,19 @@ module BELParser
 
               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))))))              
+                  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
 
@@ -72,7 +74,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|