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

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Files changed (153) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +1 -1
  3. data/VERSION +1 -1
  4. data/bin/bel2_validator +7 -4
  5. data/lib/bel_parser/ast_filter.rb +2 -2
  6. data/lib/bel_parser/ast_generator.rb +11 -18
  7. data/lib/bel_parser/language/expression_validator.rb +8 -0
  8. data/lib/bel_parser/language/quoting.rb +19 -22
  9. data/lib/bel_parser/language/semantics/deeply_nested_statement.rb +65 -0
  10. data/lib/bel_parser/language/semantics/function_deprecation.rb +36 -0
  11. data/lib/bel_parser/language/semantics/list_function_subject.rb +45 -0
  12. data/lib/bel_parser/language/semantics/relationship_deprecation.rb +36 -0
  13. data/lib/bel_parser/language/semantics/signature_mapping.rb +30 -16
  14. data/lib/bel_parser/language/semantics.rb +7 -2
  15. data/lib/bel_parser/language/semantics_ast.rb +22 -12
  16. data/lib/bel_parser/language/semantics_function.rb +4 -1
  17. data/lib/bel_parser/language/semantics_result.rb +1 -0
  18. data/lib/bel_parser/language/semantics_warning.rb +2 -0
  19. data/lib/bel_parser/language/signature.rb +3 -3
  20. data/lib/bel_parser/language/syntax/invalid_function.rb +2 -2
  21. data/lib/bel_parser/language/syntax/invalid_relationship.rb +2 -2
  22. data/lib/bel_parser/language/syntax/undefined_namespace.rb +0 -1
  23. data/lib/bel_parser/language/syntax.rb +7 -2
  24. data/lib/bel_parser/language/syntax_error.rb +2 -0
  25. data/lib/bel_parser/language/syntax_function.rb +4 -1
  26. data/lib/bel_parser/language/syntax_result.rb +1 -0
  27. data/lib/bel_parser/language/syntax_warning.rb +2 -0
  28. data/lib/bel_parser/language/version1_0/functions/abundance.rb +14 -15
  29. data/lib/bel_parser/language/version1_0/functions/biological_process.rb +14 -15
  30. data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb +25 -21
  31. data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb +15 -12
  32. data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb +15 -12
  33. data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb +25 -21
  34. data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +26 -25
  35. data/lib/bel_parser/language/version1_0/functions/composite_abundance.rb +13 -12
  36. data/lib/bel_parser/language/version1_0/functions/degradation.rb +15 -12
  37. data/lib/bel_parser/language/version1_0/functions/fusion.rb +135 -129
  38. data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +34 -34
  39. data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb +24 -21
  40. data/lib/bel_parser/language/version1_0/functions/kinase_activity.rb +25 -21
  41. data/lib/bel_parser/language/version1_0/functions/list.rb +24 -24
  42. data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +18 -17
  43. data/lib/bel_parser/language/version1_0/functions/molecular_activity.rb +14 -12
  44. data/lib/bel_parser/language/version1_0/functions/pathology.rb +14 -15
  45. data/lib/bel_parser/language/version1_0/functions/peptidase_activity.rb +23 -21
  46. data/lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb +23 -21
  47. data/lib/bel_parser/language/version1_0/functions/products.rb +9 -10
  48. data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +94 -91
  49. data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +60 -57
  50. data/lib/bel_parser/language/version1_0/functions/reactants.rb +9 -10
  51. data/lib/bel_parser/language/version1_0/functions/reaction.rb +18 -17
  52. data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb +25 -21
  53. data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +34 -34
  54. data/lib/bel_parser/language/version1_0/functions/substitution.rb +29 -28
  55. data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb +25 -21
  56. data/lib/bel_parser/language/version1_0/functions/translocation.rb +33 -32
  57. data/lib/bel_parser/language/version1_0/functions/transport_activity.rb +26 -21
  58. data/lib/bel_parser/language/version1_0/functions/truncation.rb +15 -14
  59. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +16 -2
  60. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +8 -2
  61. data/lib/bel_parser/language/version1_0/relationships/association.rb +13 -2
  62. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +9 -2
  63. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +13 -2
  64. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +22 -2
  65. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +11 -2
  66. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +11 -2
  67. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +25 -2
  68. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +20 -2
  69. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +15 -2
  70. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +20 -2
  71. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +13 -2
  72. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +15 -2
  73. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +13 -2
  74. data/lib/bel_parser/language/version1_0/relationships/includes.rb +18 -2
  75. data/lib/bel_parser/language/version1_0/relationships/increases.rb +22 -2
  76. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +15 -2
  77. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +13 -2
  78. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +15 -2
  79. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +9 -2
  80. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +11 -2
  81. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +16 -2
  82. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +15 -2
  83. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +22 -2
  84. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +12 -2
  85. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +13 -2
  86. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +16 -2
  87. data/lib/bel_parser/language/version1_0/syntax/function.rb +0 -1
  88. data/lib/bel_parser/language/version1_0.rb +13 -2
  89. data/lib/bel_parser/language/version2_0/functions/abundance.rb +54 -53
  90. data/lib/bel_parser/language/version2_0/functions/activity.rb +8 -5
  91. data/lib/bel_parser/language/version2_0/functions/biological_process.rb +16 -16
  92. data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +15 -12
  93. data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +15 -12
  94. data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +61 -58
  95. data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +13 -12
  96. data/lib/bel_parser/language/version2_0/functions/degradation.rb +15 -12
  97. data/lib/bel_parser/language/version2_0/functions/fragment.rb +8 -6
  98. data/lib/bel_parser/language/version2_0/functions/from_location.rb +18 -17
  99. data/lib/bel_parser/language/version2_0/functions/fusion.rb +120 -117
  100. data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +64 -62
  101. data/lib/bel_parser/language/version2_0/functions/list.rb +24 -24
  102. data/lib/bel_parser/language/version2_0/functions/location.rb +14 -15
  103. data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +58 -55
  104. data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +16 -14
  105. data/lib/bel_parser/language/version2_0/functions/pathology.rb +14 -15
  106. data/lib/bel_parser/language/version2_0/functions/products.rb +9 -10
  107. data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +96 -92
  108. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +57 -54
  109. data/lib/bel_parser/language/version2_0/functions/reactants.rb +9 -10
  110. data/lib/bel_parser/language/version2_0/functions/reaction.rb +18 -17
  111. data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +64 -62
  112. data/lib/bel_parser/language/version2_0/functions/to_location.rb +16 -16
  113. data/lib/bel_parser/language/version2_0/functions/translocation.rb +23 -22
  114. data/lib/bel_parser/language/version2_0/functions/variant.rb +13 -13
  115. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +16 -2
  116. data/lib/bel_parser/language/version2_0/relationships/analogous.rb +8 -2
  117. data/lib/bel_parser/language/version2_0/relationships/association.rb +13 -2
  118. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +9 -2
  119. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +13 -2
  120. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +22 -2
  121. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +11 -2
  122. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +11 -2
  123. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +25 -2
  124. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +20 -2
  125. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +15 -2
  126. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +20 -2
  127. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +13 -2
  128. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +15 -2
  129. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +13 -2
  130. data/lib/bel_parser/language/version2_0/relationships/includes.rb +18 -2
  131. data/lib/bel_parser/language/version2_0/relationships/increases.rb +22 -2
  132. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +15 -2
  133. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +13 -2
  134. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +15 -2
  135. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +9 -2
  136. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +11 -2
  137. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +16 -2
  138. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +15 -2
  139. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +14 -2
  140. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +22 -2
  141. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +12 -2
  142. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +13 -2
  143. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +16 -2
  144. data/lib/bel_parser/language.rb +18 -8
  145. data/lib/bel_parser/parser.rb +1 -0
  146. data/lib/bel_parser/parsers/ast/node.rb +112 -74
  147. data/lib/bel_parser/parsers/bel_script/set.rl +1 -1
  148. data/lib/bel_parser/parsers/bel_script/set_document.rb +7087 -0
  149. data/lib/bel_parser/parsers/bel_script/set_document.rl +97 -0
  150. data/lib/bel_parser/parsers/bel_script.rb +1 -0
  151. data/lib/bel_parser/parsers/common/common.rl +1 -1
  152. data/lib/bel_parser/script/parser.rb +1 -0
  153. metadata +8 -2
data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ProteinAbundanceWithFusionSignature
41
41
  class ProteinAbundanceWithFusionSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,24 +45,24 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(ProteinAbundance))),
51
- argument(
52
- parameter(
53
- prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
57
- value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:ProteinAbundance))))),
61
- argument(
62
- term(
63
- function(
64
- identifier(
65
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
48
+ function(
49
+ identifier(
50
+ function_of(ProteinAbundance))),
51
+ argument(
52
+ parameter(
53
+ prefix(
54
+ identifier(
55
+ has_namespace,
56
+ namespace_of(:*))),
57
+ value(
58
+ value_type(
59
+ has_encoding,
60
+ encoding_of(:ProteinAbundance))))),
61
+ argument(
62
+ term(
63
+ function(
64
+ identifier(
65
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
66
66
  end
67
67
  private_constant :AST
68
68
 
@@ -77,7 +77,8 @@ module BELParser
77
77
  STRING_FORM
78
78
  end
79
79
  end
80
-
80
+
81
+ # ProteinAbundanceWithProteinModificationSignature
81
82
  class ProteinAbundanceWithProteinModificationSignature
82
83
  extend BELParser::Language::Signature
83
84
 
@@ -85,24 +86,24 @@ module BELParser
85
86
 
86
87
  AST = BELParser::Language::Semantics::Builder.build do
87
88
  term(
88
- function(
89
- identifier(
90
- function_of(ProteinAbundance))),
91
- argument(
92
- parameter(
93
- prefix(
94
- identifier(
95
- has_namespace,
96
- namespace_of(:*))),
97
- value(
98
- value_type(
99
- has_encoding,
100
- encoding_of(:ProteinAbundance))))),
101
- argument(
102
- term(
103
- function(
104
- identifier(
105
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinModification))))))
89
+ function(
90
+ identifier(
91
+ function_of(ProteinAbundance))),
92
+ argument(
93
+ parameter(
94
+ prefix(
95
+ identifier(
96
+ has_namespace,
97
+ namespace_of(:*))),
98
+ value(
99
+ value_type(
100
+ has_encoding,
101
+ encoding_of(:ProteinAbundance))))),
102
+ argument(
103
+ term(
104
+ function(
105
+ identifier(
106
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinModification))))))
106
107
  end
107
108
  private_constant :AST
108
109
 
@@ -117,7 +118,8 @@ module BELParser
117
118
  STRING_FORM
118
119
  end
119
120
  end
120
-
121
+
122
+ # ProteinAbundanceWithSubstitutionSignature
121
123
  class ProteinAbundanceWithSubstitutionSignature
122
124
  extend BELParser::Language::Signature
123
125
 
@@ -125,24 +127,24 @@ module BELParser
125
127
 
126
128
  AST = BELParser::Language::Semantics::Builder.build do
127
129
  term(
128
- function(
129
- identifier(
130
- function_of(ProteinAbundance))),
131
- argument(
132
- parameter(
133
- prefix(
134
- identifier(
135
- has_namespace,
136
- namespace_of(:*))),
137
- value(
138
- value_type(
139
- has_encoding,
140
- encoding_of(:ProteinAbundance))))),
141
- argument(
142
- term(
143
- function(
144
- identifier(
145
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Substitution))))))
130
+ function(
131
+ identifier(
132
+ function_of(ProteinAbundance))),
133
+ argument(
134
+ parameter(
135
+ prefix(
136
+ identifier(
137
+ has_namespace,
138
+ namespace_of(:*))),
139
+ value(
140
+ value_type(
141
+ has_encoding,
142
+ encoding_of(:ProteinAbundance))))),
143
+ argument(
144
+ term(
145
+ function(
146
+ identifier(
147
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Substitution))))))
146
148
  end
147
149
  private_constant :AST
148
150
 
@@ -157,7 +159,8 @@ module BELParser
157
159
  STRING_FORM
158
160
  end
159
161
  end
160
-
162
+
163
+ # ProteinAbundanceWithTruncationSignature
161
164
  class ProteinAbundanceWithTruncationSignature
162
165
  extend BELParser::Language::Signature
163
166
 
@@ -165,24 +168,24 @@ module BELParser
165
168
 
166
169
  AST = BELParser::Language::Semantics::Builder.build do
167
170
  term(
168
- function(
169
- identifier(
170
- function_of(ProteinAbundance))),
171
- argument(
172
- parameter(
173
- prefix(
174
- identifier(
175
- has_namespace,
176
- namespace_of(:*))),
177
- value(
178
- value_type(
179
- has_encoding,
180
- encoding_of(:ProteinAbundance))))),
181
- argument(
182
- term(
183
- function(
184
- identifier(
185
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Truncation))))))
171
+ function(
172
+ identifier(
173
+ function_of(ProteinAbundance))),
174
+ argument(
175
+ parameter(
176
+ prefix(
177
+ identifier(
178
+ has_namespace,
179
+ namespace_of(:*))),
180
+ value(
181
+ value_type(
182
+ has_encoding,
183
+ encoding_of(:ProteinAbundance))))),
184
+ argument(
185
+ term(
186
+ function(
187
+ identifier(
188
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Truncation))))))
186
189
  end
187
190
  private_constant :AST
188
191
 
@@ -197,7 +200,8 @@ module BELParser
197
200
  STRING_FORM
198
201
  end
199
202
  end
200
-
203
+
204
+ # ProteinAbundanceSignature
201
205
  class ProteinAbundanceSignature
202
206
  extend BELParser::Language::Signature
203
207
 
@@ -205,19 +209,19 @@ module BELParser
205
209
 
206
210
  AST = BELParser::Language::Semantics::Builder.build do
207
211
  term(
208
- function(
209
- identifier(
210
- function_of(ProteinAbundance))),
211
- argument(
212
- parameter(
213
- prefix(
214
- identifier(
215
- has_namespace,
216
- namespace_of(:*))),
217
- value(
218
- value_type(
219
- has_encoding,
220
- encoding_of(:ProteinAbundance))))))
212
+ function(
213
+ identifier(
214
+ function_of(ProteinAbundance))),
215
+ argument(
216
+ parameter(
217
+ prefix(
218
+ identifier(
219
+ has_namespace,
220
+ namespace_of(:*))),
221
+ value(
222
+ value_type(
223
+ has_encoding,
224
+ encoding_of(:ProteinAbundance))))))
221
225
  end
222
226
  private_constant :AST
223
227
 
@@ -232,7 +236,6 @@ module BELParser
232
236
  STRING_FORM
233
237
  end
234
238
  end
235
-
236
239
  end
237
240
 
238
241
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/protein_modification.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # ProteinModification: Denotes a covalently modified protein abundance
10
+ # ProteinModification: Denotes a covalently modified protein
11
+ # abundance
11
12
  class ProteinModification
12
13
  extend Function
13
14
 
14
15
  SHORT = :pmod
15
16
  LONG = :proteinModification
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinModification
17
- DESCRIPTION = 'Denotes a covalently modified protein abundance'.freeze
18
+ DESCRIPTION = 'Denotes a covalently modified protein
19
+ bundance'.freeze
18
20
 
19
21
  def self.short
20
22
  SHORT
@@ -37,7 +39,7 @@ module BELParser
37
39
  end
38
40
 
39
41
  module Signatures
40
-
42
+ # ProteinModificationWithCovalentAminoPositionSignature
41
43
  class ProteinModificationWithCovalentAminoPositionSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,30 +47,30 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(ProteinModification))),
51
- argument(
52
- parameter(
53
- prefix(
54
- any),
55
- value(
56
- value_type(
57
- encoding_of(:*))))),
58
- argument(
59
- parameter(
60
- prefix(
61
- any),
62
- value(
63
- value_type(
64
- encoding_of(:*))))),
65
- argument(
66
- parameter(
67
- prefix(
68
- any),
69
- value(
70
- value_type(
71
- encoding_of(:*))))))
50
+ function(
51
+ identifier(
52
+ function_of(ProteinModification))),
53
+ argument(
54
+ parameter(
55
+ prefix(
56
+ any),
57
+ value(
58
+ value_type(
59
+ encoding_of(:*))))),
60
+ argument(
61
+ parameter(
62
+ prefix(
63
+ any),
64
+ value(
65
+ value_type(
66
+ encoding_of(:*))))),
67
+ argument(
68
+ parameter(
69
+ prefix(
70
+ any),
71
+ value(
72
+ value_type(
73
+ encoding_of(:*))))))
72
74
  end
73
75
  private_constant :AST
74
76
 
@@ -83,7 +85,8 @@ module BELParser
83
85
  STRING_FORM
84
86
  end
85
87
  end
86
-
88
+
89
+ # ProteinModificationWithCovalentAminoSignature
87
90
  class ProteinModificationWithCovalentAminoSignature
88
91
  extend BELParser::Language::Signature
89
92
 
@@ -91,23 +94,23 @@ module BELParser
91
94
 
92
95
  AST = BELParser::Language::Semantics::Builder.build do
93
96
  term(
94
- function(
95
- identifier(
96
- function_of(ProteinModification))),
97
- argument(
98
- parameter(
99
- prefix(
100
- any),
101
- value(
102
- value_type(
103
- encoding_of(:*))))),
104
- argument(
105
- parameter(
106
- prefix(
107
- any),
108
- value(
109
- value_type(
110
- encoding_of(:*))))))
97
+ function(
98
+ identifier(
99
+ function_of(ProteinModification))),
100
+ argument(
101
+ parameter(
102
+ prefix(
103
+ any),
104
+ value(
105
+ value_type(
106
+ encoding_of(:*))))),
107
+ argument(
108
+ parameter(
109
+ prefix(
110
+ any),
111
+ value(
112
+ value_type(
113
+ encoding_of(:*))))))
111
114
  end
112
115
  private_constant :AST
113
116
 
@@ -122,7 +125,8 @@ module BELParser
122
125
  STRING_FORM
123
126
  end
124
127
  end
125
-
128
+
129
+ # ProteinModificationWithCovalentSignature
126
130
  class ProteinModificationWithCovalentSignature
127
131
  extend BELParser::Language::Signature
128
132
 
@@ -130,16 +134,16 @@ module BELParser
130
134
 
131
135
  AST = BELParser::Language::Semantics::Builder.build do
132
136
  term(
133
- function(
134
- identifier(
135
- function_of(ProteinModification))),
136
- argument(
137
- parameter(
138
- prefix(
139
- any),
140
- value(
141
- value_type(
142
- encoding_of(:*))))))
137
+ function(
138
+ identifier(
139
+ function_of(ProteinModification))),
140
+ argument(
141
+ parameter(
142
+ prefix(
143
+ any),
144
+ value(
145
+ value_type(
146
+ encoding_of(:*))))))
143
147
  end
144
148
  private_constant :AST
145
149
 
@@ -154,7 +158,6 @@ module BELParser
154
158
  STRING_FORM
155
159
  end
156
160
  end
157
-
158
161
  end
159
162
 
160
163
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/reactants.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ReactantsSignature
41
41
  class ReactantsSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,14 +45,14 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(Reactants))),
51
- variadic_arguments(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
48
+ function(
49
+ identifier(
50
+ function_of(Reactants))),
51
+ variadic_arguments(
52
+ term(
53
+ function(
54
+ identifier(
55
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
56
56
  end
57
57
  private_constant :AST
58
58
 
@@ -67,7 +67,6 @@ module BELParser
67
67
  STRING_FORM
68
68
  end
69
69
  end
70
-
71
70
  end
72
71
 
73
72
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/reaction.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # Reaction: Denotes the frequency or abundance of events in a reaction
10
+ # Reaction: Denotes the frequency or abundance of events in
11
+ # a reaction
11
12
  class Reaction
12
13
  extend Function
13
14
 
14
15
  SHORT = :rxn
15
16
  LONG = :reaction
16
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in a reaction'.freeze
18
+ DESCRIPTION = 'Denotes the frequency or abundance of events
19
+ n a reaction'.freeze
18
20
 
19
21
  def self.short
20
22
  SHORT
@@ -37,7 +39,7 @@ module BELParser
37
39
  end
38
40
 
39
41
  module Signatures
40
-
42
+ # ReactionSignature
41
43
  class ReactionSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,19 +47,19 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(Reaction))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
56
- argument(
57
- term(
58
- function(
59
- identifier(
60
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
50
+ function(
51
+ identifier(
52
+ function_of(Reaction))),
53
+ argument(
54
+ term(
55
+ function(
56
+ identifier(
57
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
58
+ argument(
59
+ term(
60
+ function(
61
+ identifier(
62
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
61
63
  end
62
64
  private_constant :AST
63
65
 
@@ -72,7 +74,6 @@ module BELParser
72
74
  STRING_FORM
73
75
  end
74
76
  end
75
-
76
77
  end
77
78
 
78
79
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb CHANGED
@@ -7,14 +7,18 @@ module BELParser
7
7
  module Language
8
8
  module Version1_0
9
9
  module Functions
10
- # RibosylationActivity: Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins
10
+ # RibosylationActivity: Denotes the frequency or abundance of
11
+ # events in which a member acts to perform post-translational
12
+ # modification of proteins
11
13
  class RibosylationActivity
12
14
  extend Function
13
15
 
14
16
  SHORT = :ribo
15
17
  LONG = :ribosylationActivity
16
18
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::RibosylationActivity
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins'.freeze
19
+ DESCRIPTION = 'Denotes the frequency or abundance of events in
20
+ hich a member acts to perform post-translational
21
+ odification of proteins'.freeze
18
22
 
19
23
  def self.short
20
24
  SHORT
@@ -37,7 +41,7 @@ module BELParser
37
41
  end
38
42
 
39
43
  module Signatures
40
-
44
+ # RibosylationActivityWithComplexAbundanceSignature
41
45
  class RibosylationActivityWithComplexAbundanceSignature
42
46
  extend BELParser::Language::Signature
43
47
 
@@ -45,14 +49,14 @@ module BELParser
45
49
 
46
50
  AST = BELParser::Language::Semantics::Builder.build do
47
51
  term(
48
- function(
49
- identifier(
50
- function_of(RibosylationActivity))),
51
- argument(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
52
+ function(
53
+ identifier(
54
+ function_of(RibosylationActivity))),
55
+ argument(
56
+ term(
57
+ function(
58
+ identifier(
59
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
56
60
  end
57
61
  private_constant :AST
58
62
 
@@ -67,7 +71,8 @@ module BELParser
67
71
  STRING_FORM
68
72
  end
69
73
  end
70
-
74
+
75
+ # RibosylationActivityWithProteinAbundanceSignature
71
76
  class RibosylationActivityWithProteinAbundanceSignature
72
77
  extend BELParser::Language::Signature
73
78
 
@@ -75,14 +80,14 @@ module BELParser
75
80
 
76
81
  AST = BELParser::Language::Semantics::Builder.build do
77
82
  term(
78
- function(
79
- identifier(
80
- function_of(RibosylationActivity))),
81
- argument(
82
- term(
83
- function(
84
- identifier(
85
- return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
83
+ function(
84
+ identifier(
85
+ function_of(RibosylationActivity))),
86
+ argument(
87
+ term(
88
+ function(
89
+ identifier(
90
+ return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
86
91
  end
87
92
  private_constant :AST
88
93
 
@@ -97,7 +102,6 @@ module BELParser
97
102
  STRING_FORM
98
103
  end
99
104
  end
100
-
101
105
  end
102
106
 
103
107
  SIGNATURES = Signatures.constants.map do |const|