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/version2_0/functions/fusion.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version2_0
9
9
  module Functions
10
- # Fusion: Specifies the abundance of a protein translated from the fusion of a gene.
10
+ # Fusion: Specifies the abundance of a protein translated from
11
+ # the fusion of a gene.
11
12
  class Fusion
12
13
  extend Function
13
14
 
14
15
  SHORT = :fus
15
16
  LONG = :fusion
16
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fusion
17
- DESCRIPTION = 'Specifies the abundance of a protein translated from the fusion of a gene.'.freeze
18
+ DESCRIPTION = 'Specifies the abundance of a protein translated
19
+ rom the fusion of a gene.'.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
+ # FusionWithGeneEncodingSignature
41
43
  class FusionWithGeneEncodingSignature
42
44
  extend BELParser::Language::Signature
43
45
 
@@ -45,43 +47,43 @@ module BELParser
45
47
 
46
48
  AST = BELParser::Language::Semantics::Builder.build do
47
49
  term(
48
- function(
49
- identifier(
50
- function_of(Fusion))),
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(:GeneAbundance))))),
61
- argument(
62
- parameter(
63
- prefix(
64
- any),
65
- value(
66
- value_type(
67
- encoding_of(:*))))),
68
- argument(
69
- parameter(
70
- prefix(
71
- identifier(
72
- has_namespace,
73
- namespace_of(:*))),
74
- value(
75
- value_type(
76
- has_encoding,
77
- encoding_of(:GeneAbundance))))),
78
- argument(
79
- parameter(
80
- prefix(
81
- any),
82
- value(
83
- value_type(
84
- encoding_of(:*))))))
50
+ function(
51
+ identifier(
52
+ function_of(Fusion))),
53
+ argument(
54
+ parameter(
55
+ prefix(
56
+ identifier(
57
+ has_namespace,
58
+ namespace_of(:*))),
59
+ value(
60
+ value_type(
61
+ has_encoding,
62
+ encoding_of(:GeneAbundance))))),
63
+ argument(
64
+ parameter(
65
+ prefix(
66
+ any),
67
+ value(
68
+ value_type(
69
+ encoding_of(:*))))),
70
+ argument(
71
+ parameter(
72
+ prefix(
73
+ identifier(
74
+ has_namespace,
75
+ namespace_of(:*))),
76
+ value(
77
+ value_type(
78
+ has_encoding,
79
+ encoding_of(:GeneAbundance))))),
80
+ argument(
81
+ parameter(
82
+ prefix(
83
+ any),
84
+ value(
85
+ value_type(
86
+ encoding_of(:*))))))
85
87
  end
86
88
  private_constant :AST
87
89
 
@@ -96,7 +98,8 @@ module BELParser
96
98
  STRING_FORM
97
99
  end
98
100
  end
99
-
101
+
102
+ # FusionWithProteinEncodingSignature
100
103
  class FusionWithProteinEncodingSignature
101
104
  extend BELParser::Language::Signature
102
105
 
@@ -104,43 +107,43 @@ module BELParser
104
107
 
105
108
  AST = BELParser::Language::Semantics::Builder.build do
106
109
  term(
107
- function(
108
- identifier(
109
- function_of(Fusion))),
110
- argument(
111
- parameter(
112
- prefix(
113
- identifier(
114
- has_namespace,
115
- namespace_of(:*))),
116
- value(
117
- value_type(
118
- has_encoding,
119
- encoding_of(:ProteinAbundance))))),
120
- argument(
121
- parameter(
122
- prefix(
123
- any),
124
- value(
125
- value_type(
126
- encoding_of(:*))))),
127
- argument(
128
- parameter(
129
- prefix(
130
- identifier(
131
- has_namespace,
132
- namespace_of(:*))),
133
- value(
134
- value_type(
135
- has_encoding,
136
- encoding_of(:ProteinAbundance))))),
137
- argument(
138
- parameter(
139
- prefix(
140
- any),
141
- value(
142
- value_type(
143
- encoding_of(:*))))))
110
+ function(
111
+ identifier(
112
+ function_of(Fusion))),
113
+ argument(
114
+ parameter(
115
+ prefix(
116
+ identifier(
117
+ has_namespace,
118
+ namespace_of(:*))),
119
+ value(
120
+ value_type(
121
+ has_encoding,
122
+ encoding_of(:ProteinAbundance))))),
123
+ argument(
124
+ parameter(
125
+ prefix(
126
+ any),
127
+ value(
128
+ value_type(
129
+ encoding_of(:*))))),
130
+ argument(
131
+ parameter(
132
+ prefix(
133
+ identifier(
134
+ has_namespace,
135
+ namespace_of(:*))),
136
+ value(
137
+ value_type(
138
+ has_encoding,
139
+ encoding_of(:ProteinAbundance))))),
140
+ argument(
141
+ parameter(
142
+ prefix(
143
+ any),
144
+ value(
145
+ value_type(
146
+ encoding_of(:*))))))
144
147
  end
145
148
  private_constant :AST
146
149
 
@@ -155,7 +158,8 @@ module BELParser
155
158
  STRING_FORM
156
159
  end
157
160
  end
158
-
161
+
162
+ # FusionWithRNAEncodingSignature
159
163
  class FusionWithRNAEncodingSignature
160
164
  extend BELParser::Language::Signature
161
165
 
@@ -163,43 +167,43 @@ module BELParser
163
167
 
164
168
  AST = BELParser::Language::Semantics::Builder.build do
165
169
  term(
166
- function(
167
- identifier(
168
- function_of(Fusion))),
169
- argument(
170
- parameter(
171
- prefix(
172
- identifier(
173
- has_namespace,
174
- namespace_of(:*))),
175
- value(
176
- value_type(
177
- has_encoding,
178
- encoding_of(:RnaAbundance))))),
179
- argument(
180
- parameter(
181
- prefix(
182
- any),
183
- value(
184
- value_type(
185
- encoding_of(:*))))),
186
- argument(
187
- parameter(
188
- prefix(
189
- identifier(
190
- has_namespace,
191
- namespace_of(:*))),
192
- value(
193
- value_type(
194
- has_encoding,
195
- encoding_of(:RnaAbundance))))),
196
- argument(
197
- parameter(
198
- prefix(
199
- any),
200
- value(
201
- value_type(
202
- encoding_of(:*))))))
170
+ function(
171
+ identifier(
172
+ function_of(Fusion))),
173
+ argument(
174
+ parameter(
175
+ prefix(
176
+ identifier(
177
+ has_namespace,
178
+ namespace_of(:*))),
179
+ value(
180
+ value_type(
181
+ has_encoding,
182
+ encoding_of(:RnaAbundance))))),
183
+ argument(
184
+ parameter(
185
+ prefix(
186
+ any),
187
+ value(
188
+ value_type(
189
+ encoding_of(:*))))),
190
+ argument(
191
+ parameter(
192
+ prefix(
193
+ identifier(
194
+ has_namespace,
195
+ namespace_of(:*))),
196
+ value(
197
+ value_type(
198
+ has_encoding,
199
+ encoding_of(:RnaAbundance))))),
200
+ argument(
201
+ parameter(
202
+ prefix(
203
+ any),
204
+ value(
205
+ value_type(
206
+ encoding_of(:*))))))
203
207
  end
204
208
  private_constant :AST
205
209
 
@@ -214,7 +218,6 @@ module BELParser
214
218
  STRING_FORM
215
219
  end
216
220
  end
217
-
218
221
  end
219
222
 
220
223
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # GeneAbundanceSignature
41
41
  class GeneAbundanceSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,19 +45,19 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(GeneAbundance))),
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(:GeneAbundance))))))
48
+ function(
49
+ identifier(
50
+ function_of(GeneAbundance))),
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(:GeneAbundance))))))
61
61
  end
62
62
  private_constant :AST
63
63
 
@@ -72,7 +72,8 @@ module BELParser
72
72
  STRING_FORM
73
73
  end
74
74
  end
75
-
75
+
76
+ # GeneAbundanceWithFusionSignature
76
77
  class GeneAbundanceWithFusionSignature
77
78
  extend BELParser::Language::Signature
78
79
 
@@ -80,14 +81,14 @@ module BELParser
80
81
 
81
82
  AST = BELParser::Language::Semantics::Builder.build do
82
83
  term(
83
- function(
84
- identifier(
85
- function_of(GeneAbundance))),
86
- argument(
87
- term(
88
- function(
89
- identifier(
90
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
84
+ function(
85
+ identifier(
86
+ function_of(GeneAbundance))),
87
+ argument(
88
+ term(
89
+ function(
90
+ identifier(
91
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
91
92
  end
92
93
  private_constant :AST
93
94
 
@@ -102,7 +103,8 @@ module BELParser
102
103
  STRING_FORM
103
104
  end
104
105
  end
105
-
106
+
107
+ # GeneAbundanceWithLocationSignature
106
108
  class GeneAbundanceWithLocationSignature
107
109
  extend BELParser::Language::Signature
108
110
 
@@ -110,24 +112,24 @@ module BELParser
110
112
 
111
113
  AST = BELParser::Language::Semantics::Builder.build do
112
114
  term(
113
- function(
114
- identifier(
115
- function_of(GeneAbundance))),
116
- argument(
117
- parameter(
118
- prefix(
119
- identifier(
120
- has_namespace,
121
- namespace_of(:*))),
122
- value(
123
- value_type(
124
- has_encoding,
125
- encoding_of(:Abundance))))),
126
- argument(
127
- term(
128
- function(
129
- identifier(
130
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
115
+ function(
116
+ identifier(
117
+ function_of(GeneAbundance))),
118
+ argument(
119
+ parameter(
120
+ prefix(
121
+ identifier(
122
+ has_namespace,
123
+ namespace_of(:*))),
124
+ value(
125
+ value_type(
126
+ has_encoding,
127
+ encoding_of(:Abundance))))),
128
+ argument(
129
+ term(
130
+ function(
131
+ identifier(
132
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
131
133
  end
132
134
  private_constant :AST
133
135
 
@@ -142,7 +144,8 @@ module BELParser
142
144
  STRING_FORM
143
145
  end
144
146
  end
145
-
147
+
148
+ # GeneAbundanceWithVariantSignature
146
149
  class GeneAbundanceWithVariantSignature
147
150
  extend BELParser::Language::Signature
148
151
 
@@ -150,24 +153,24 @@ module BELParser
150
153
 
151
154
  AST = BELParser::Language::Semantics::Builder.build do
152
155
  term(
153
- function(
154
- identifier(
155
- function_of(GeneAbundance))),
156
- argument(
157
- parameter(
158
- prefix(
159
- identifier(
160
- has_namespace,
161
- namespace_of(:*))),
162
- value(
163
- value_type(
164
- has_encoding,
165
- encoding_of(:GeneAbundance))))),
166
- argument(
167
- term(
168
- function(
169
- identifier(
170
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
156
+ function(
157
+ identifier(
158
+ function_of(GeneAbundance))),
159
+ argument(
160
+ parameter(
161
+ prefix(
162
+ identifier(
163
+ has_namespace,
164
+ namespace_of(:*))),
165
+ value(
166
+ value_type(
167
+ has_encoding,
168
+ encoding_of(:GeneAbundance))))),
169
+ argument(
170
+ term(
171
+ function(
172
+ identifier(
173
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
171
174
  end
172
175
  private_constant :AST
173
176
 
@@ -182,7 +185,6 @@ module BELParser
182
185
  STRING_FORM
183
186
  end
184
187
  end
185
-
186
188
  end
187
189
 
188
190
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/list.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ListOfAbundanceEncodingSignature
41
41
  class ListOfAbundanceEncodingSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,19 +45,19 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(List))),
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(:Abundance))))))
48
+ function(
49
+ identifier(
50
+ function_of(List))),
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(:Abundance))))))
61
61
  end
62
62
  private_constant :AST
63
63
 
@@ -72,7 +72,8 @@ module BELParser
72
72
  STRING_FORM
73
73
  end
74
74
  end
75
-
75
+
76
+ # ListOfAbundanceSignature
76
77
  class ListOfAbundanceSignature
77
78
  extend BELParser::Language::Signature
78
79
 
@@ -80,14 +81,14 @@ module BELParser
80
81
 
81
82
  AST = BELParser::Language::Semantics::Builder.build do
82
83
  term(
83
- function(
84
- identifier(
85
- function_of(List))),
86
- variadic_arguments(
87
- term(
88
- function(
89
- identifier(
90
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
84
+ function(
85
+ identifier(
86
+ function_of(List))),
87
+ variadic_arguments(
88
+ term(
89
+ function(
90
+ identifier(
91
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
91
92
  end
92
93
  private_constant :AST
93
94
 
@@ -102,7 +103,6 @@ module BELParser
102
103
  STRING_FORM
103
104
  end
104
105
  end
105
-
106
106
  end
107
107
 
108
108
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/location.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # LocationSignature
41
41
  class LocationSignature
42
42
  extend BELParser::Language::Signature
43
43
 
@@ -45,19 +45,19 @@ module BELParser
45
45
 
46
46
  AST = BELParser::Language::Semantics::Builder.build do
47
47
  term(
48
- function(
49
- identifier(
50
- function_of(Location))),
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(:Location))))))
48
+ function(
49
+ identifier(
50
+ function_of(Location))),
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(:Location))))))
61
61
  end
62
62
  private_constant :AST
63
63
 
@@ -72,7 +72,6 @@ module BELParser
72
72
  STRING_FORM
73
73
  end
74
74
  end
75
-
76
75
  end
77
76
 
78
77
  SIGNATURES = Signatures.constants.map do |const|