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

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

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # KinaseActivity: Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate
+        # KinaseActivity: Denotes the frequency or abundance of events
+        # in which a member acts as a kinase, performing enzymatic
+        # phosphorylation of a substrate
         class KinaseActivity
           extend Function
 
           SHORT       = :kin
           LONG        = :kinaseActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::KinaseActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a kinase, performing
+          nzymatic phosphorylation of a substrate'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # KinaseActivityOfComplexAbundanceSignature
             class KinaseActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(KinaseActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(KinaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # KinaseActivityOfProteinAbundanceSignature
             class KinaseActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +80,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(KinaseActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(KinaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +102,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # ListOfAbundanceEncodingSignature
             class ListOfAbundanceEncodingSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +45,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(List))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(List))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))))
               end
               private_constant :AST
 
@@ -72,7 +72,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # ListOfAbundanceSignature
             class ListOfAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -80,14 +81,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(List))),
-                variadic_arguments(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(List))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -102,7 +103,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # MicroRNAAbundance: Denotes the abundance of a processed, functional microRNA
+        # MicroRNAAbundance: Denotes the abundance of a processed,
+        # functional microRNA
         class MicroRNAAbundance
           extend Function
 
           SHORT       = :m
           LONG        = :microRNAAbundance
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MicroRNAAbundance
-          DESCRIPTION = 'Denotes the abundance of a processed, functional microRNA'.freeze
+          DESCRIPTION = 'Denotes the abundance of a processed, functional
+          icroRNA'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # MicroRNAAbundanceSignature
             class MicroRNAAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +47,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(MicroRNAAbundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:MicroRNAAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(MicroRNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:MicroRNAAbundance))))))
               end
               private_constant :AST
 
@@ -72,7 +74,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,17 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # MolecularActivity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale
+        # MolecularActivity: Denotes the frequency or abundance of events
+        # in which a member acts as a causal agent at the molecular scale
         class MolecularActivity
           extend Function
 
           SHORT       = :act
           LONG        = :molecularActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MolecularActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a causal agent at the
+          olecular scale'.freeze
 
           def self.short
             SHORT
@@ -37,7 +40,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # MolecularActivityOfAbundanceSignature
             class MolecularActivityOfAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +48,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(MolecularActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(MolecularActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +70,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # PathologySignature
             class PathologySignature
               extend BELParser::Language::Signature
 
@@ -45,19 +45,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Pathology))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Pathology))))))              
+                  function(
+                    identifier(
+                      function_of(Pathology))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Pathology))))))
               end
               private_constant :AST
 
@@ -72,7 +72,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # PeptidaseActivity: Denotes the frequency or abundance of events in which a member acts to cleave a protein
+        # PeptidaseActivity: Denotes the frequency or abundance of events
+        # in which a member acts to cleave a protein
         class PeptidaseActivity
           extend Function
 
           SHORT       = :pep
           LONG        = :peptidaseActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PeptidaseActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to cleave a protein'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts to cleave a protein'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # PeptidaseActivityOfComplexAbundanceSignature
             class PeptidaseActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +47,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(PeptidaseActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(PeptidaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +69,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # PeptidaseActivityOfProteinAbundanceSignature
             class PeptidaseActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +78,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(PeptidaseActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(PeptidaseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +100,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # PhosphataseActivity: Denotes the frequency or abundance of events in which a member acts as a phosphatase
+        # PhosphataseActivity: Denotes the frequency or abundance of
+        # events in which a member acts as a phosphatase
         class PhosphataseActivity
           extend Function
 
           SHORT       = :phos
           LONG        = :phosphataseActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PhosphataseActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a phosphatase'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a phosphatase'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # PhosphataseActivityOfComplexAbundanceSignature
             class PhosphataseActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +47,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(PhosphataseActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(PhosphataseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +69,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # PhosphataseActivityOfProteinAbundanceSignature
             class PhosphataseActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +78,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(PhosphataseActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(PhosphataseActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +100,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

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

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # ProductsSignature
             class ProductsSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +45,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Products))),
-                variadic_arguments(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(Products))),
+                  variadic_arguments(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +67,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|