bel_parser 1.0.0.alpha.11 → 1.0.0.alpha.12

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a018453c3f5a83b1ec952460c58462f9086b05c5
+  metadata.gz: b28b03b903a5a3a1a62f4c36063c81292714cbd6
+  data.tar.gz: 631a26bb0628a77abc19f4c35a028b6851939838
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+  data.tar.gz: 2349ecf4f921f28c9b9431cd9b6f66369b46e94aa3dc27eb27c0f95f5945ce1e98eb686bd4538bf85fbc2c7c65de66292b10b82afb38d0068723bf7d68e240f6

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-04-14}
+  spec.date                  = %q{2016-04-15}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.11
+1.0.0.alpha.12

data/lib/bel_parser/language/covalent_protein_modification.rb

@@ -0,0 +1,56 @@
+module BELParser
+  module Language
+    # CovalentProteinModification defines a controlled vocabulary of
+    # post-translational protein modifications.
+    #
+    # see https://en.wikipedia.org/wiki/Post-translational_modification
+    module CovalentProteinModification
+      Acetylation     = [:Acetylation, :A].freeze
+      Farnesylation   = [:Farnesylation, :F].freeze
+      Glycosylation   = [:Glycosylation, :G].freeze
+      Hydroxylation   = [:Hydroxylation, :H].freeze
+      Methylation     = [:Methylation, :M].freeze
+      Phosphorylation = [:Phosphorylation, :P].freeze
+      Ribosylation    = [:Ribosylation, :R].freeze
+      Sumoylation     = [:Sumoylation, :S].freeze
+      Ubiquitination  = [:Ubiquitination, :U].freeze
+
+      # Determines if +sym+ represents a covalent protein modification.
+      #
+      # @param [#to_sym] sym covalent protein modification code
+      # @return [Boolean] +true+ if +sym+ code is included in supported
+      # covalent protein modifications; +false+ if not supported
+      def self.includes?(sym)
+        @hash.key?(sym.to_sym)
+      end
+
+      # Gets all supported covalent protein modification.
+      def self.names
+        @names
+      end
+
+      # Gets all supported covalent protein modification (i.e. name, 1-Letter).
+      def self.values
+        @values
+      end
+
+      unless defined? @hash
+        @hash = {}
+        constants.map(&method(:const_get)).each do |values|
+          @hash.update(
+            Hash[values.map { |v| [v, values.first] }]
+          )
+        end
+        @hash.freeze
+      end
+
+      unless defined? @names
+        @names = constants.map(&method(:const_get)).map(&:first).sort.freeze
+      end
+
+      unless defined? @values
+        @values = constants.map(&method(:const_get)).map(&:to_a).flatten.freeze
+      end
+    end
+  end
+end

data/lib/bel_parser/language/semantics_ast.rb

@@ -154,8 +154,8 @@ module BELParser
           SemanticEncodingOf.new(encoding_types, **properties)
         end
 
-        def covalent_modification_of(*covalent_mod_types, **properties)
-          SemanticCovalentModificationOf.new(covalent_mod_types, **properties)
+        def covalent_protein_modification_of(*mod_types, **properties)
+          SemanticCovalentProteinModificationOf.new(mod_types, **properties)
         end
 
         def amino_acid_of(*amino_acids, **properties)
@@ -546,14 +546,14 @@ module BELParser
         end
       end
 
-      # AST node for CovalentModificationOf is a semantic AST.
-      class SemanticCovalentModificationOf < SemanticASTNode
-        def initialize(covalent_mod_types, **properties)
-          properties[:hashed] = Hash[covalent_mod_types.map { |t| [t, true] }]
-          super(:covalent_modification_of, covalent_mod_types, properties)
+      # AST node for CovalentProteinModificationOf is a semantic AST.
+      class SemanticCovalentProteinModificationOf < SemanticASTNode
+        def initialize(mod_types, **properties)
+          properties[:hashed] = Hash[mod_types.map { |t| [t, true] }]
+          super(:covalent_protein_modification_of, mod_types, properties)
         end
 
-        def covalent_mod_types
+        def covalent_protein_modification_types
           children
         end
 

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

@@ -2,6 +2,7 @@ require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
 require_relative '../../amino_acid'
+require_relative '../../covalent_protein_modification'
 require_relative '../../semantics'
 
 module BELParser
@@ -15,7 +16,8 @@ module BELParser
 
           SHORT       = :pmod
           LONG        = :proteinModification
-          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinModification
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::
+            ProteinModification
           DESCRIPTION = 'Denotes a covalently modified protein
           bundance'.freeze
 
@@ -57,7 +59,8 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          covalent_protein_modification_of(
+                            *CovalentProteinModification.values))))),
                   argument(
                     parameter(
                       prefix(
@@ -76,8 +79,12 @@ module BELParser
               private_constant :AST
 
               STRING_FORM =
-                'proteinModification(E:*,T:AminoAcid,E:*)proteinModification'
-                .freeze
+                <<-SIG.delete("\s\n").freeze
+                proteinModification(
+                  T:CovalentProteinModification,
+                  T:AminoAcid,
+                  T:SequencePosition)proteinModification
+                SIG
               private_constant :STRING_FORM
 
               def self.semantic_ast
@@ -106,7 +113,8 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))),
+                          covalent_protein_modification_of(
+                            *CovalentProteinModification.values))))),
                   argument(
                     parameter(
                       prefix(
@@ -118,8 +126,11 @@ module BELParser
               private_constant :AST
 
               STRING_FORM =
-                'proteinModification(E:*,T:AminoAcid)proteinModification'
-                .freeze
+                <<-SIG.delete("\s\n").freeze
+                proteinModification(
+                  T:CovalentProteinModification,
+                  T:AminoAcid)proteinModification
+                SIG
               private_constant :STRING_FORM
 
               def self.semantic_ast
@@ -148,11 +159,16 @@ module BELParser
                         any),
                       value(
                         value_type(
-                          encoding_of(:*))))))
+                          covalent_protein_modification_of(
+                            *CovalentProteinModification.values))))))
               end
               private_constant :AST
 
-              STRING_FORM = 'proteinModification(E:*)proteinModification'.freeze
+              STRING_FORM =
+                <<-SIG.delete("\s\n").freeze
+                proteinModification(
+                  T:CovalentProteinModification)proteinModification
+                SIG
               private_constant :STRING_FORM
 
               def self.semantic_ast

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.11
+  version: 1.0.0.alpha.12
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-14 00:00:00.000000000 Z
+date: 2016-04-15 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
@@ -31,6 +31,7 @@ files:
 - lib/bel_parser/expression/validator.rb
 - lib/bel_parser/language.rb
 - lib/bel_parser/language/amino_acid.rb
+- lib/bel_parser/language/covalent_protein_modification.rb
 - lib/bel_parser/language/expression_validator.rb
 - lib/bel_parser/language/function.rb
 - lib/bel_parser/language/quoting.rb