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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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/micro_rna_abundance.rb CHANGED
@@ -7,14 +7,16 @@ module BELParser
7
7
  module Language
8
8
  module Version2_0
9
9
  module Functions
10
- # MicroRNAAbundance: Denotes the abundance of a processed, functional microRNA
10
+ # MicroRNAAbundance: Denotes the abundance of a processed,
11
+ # functional microRNA
11
12
  class MicroRNAAbundance
12
13
  extend Function
13
14
 
14
15
  SHORT = :m
15
16
  LONG = :microRNAAbundance
16
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
17
- DESCRIPTION = 'Denotes the abundance of a processed, functional microRNA'.freeze
18
+ DESCRIPTION = 'Denotes the abundance of a processed, functional
19
+ icroRNA'.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
+ # MicroRNAAbundanceSignature
41
43
  class MicroRNAAbundanceSignature
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(MicroRNAAbundance))),
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(:MicroRNAAbundance))))))
50
+ function(
51
+ identifier(
52
+ function_of(MicroRNAAbundance))),
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(:MicroRNAAbundance))))))
61
63
  end
62
64
  private_constant :AST
63
65
 
@@ -72,7 +74,8 @@ module BELParser
72
74
  STRING_FORM
73
75
  end
74
76
  end
75
-
77
+
78
+ # MicroRNAAbundanceWithLocationSignature
76
79
  class MicroRNAAbundanceWithLocationSignature
77
80
  extend BELParser::Language::Signature
78
81
 
@@ -80,24 +83,24 @@ module BELParser
80
83
 
81
84
  AST = BELParser::Language::Semantics::Builder.build do
82
85
  term(
83
- function(
84
- identifier(
85
- function_of(MicroRNAAbundance))),
86
- argument(
87
- parameter(
88
- prefix(
89
- identifier(
90
- has_namespace,
91
- namespace_of(:*))),
92
- value(
93
- value_type(
94
- has_encoding,
95
- encoding_of(:MicroRNAAbundance))))),
96
- argument(
97
- term(
98
- function(
99
- identifier(
100
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
86
+ function(
87
+ identifier(
88
+ function_of(MicroRNAAbundance))),
89
+ argument(
90
+ parameter(
91
+ prefix(
92
+ identifier(
93
+ has_namespace,
94
+ namespace_of(:*))),
95
+ value(
96
+ value_type(
97
+ has_encoding,
98
+ encoding_of(:MicroRNAAbundance))))),
99
+ argument(
100
+ term(
101
+ function(
102
+ identifier(
103
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
101
104
  end
102
105
  private_constant :AST
103
106
 
@@ -112,7 +115,8 @@ module BELParser
112
115
  STRING_FORM
113
116
  end
114
117
  end
115
-
118
+
119
+ # MicroRNAAbundanceWithVariantSignature
116
120
  class MicroRNAAbundanceWithVariantSignature
117
121
  extend BELParser::Language::Signature
118
122
 
@@ -120,24 +124,24 @@ module BELParser
120
124
 
121
125
  AST = BELParser::Language::Semantics::Builder.build do
122
126
  term(
123
- function(
124
- identifier(
125
- function_of(MicroRNAAbundance))),
126
- argument(
127
- parameter(
128
- prefix(
129
- identifier(
130
- has_namespace,
131
- namespace_of(:*))),
132
- value(
133
- value_type(
134
- has_encoding,
135
- encoding_of(:MicroRNAAbundance))))),
136
- argument(
137
- term(
138
- function(
139
- identifier(
140
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
127
+ function(
128
+ identifier(
129
+ function_of(MicroRNAAbundance))),
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(:MicroRNAAbundance))))),
140
+ argument(
141
+ term(
142
+ function(
143
+ identifier(
144
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
141
145
  end
142
146
  private_constant :AST
143
147
 
@@ -152,7 +156,6 @@ module BELParser
152
156
  STRING_FORM
153
157
  end
154
158
  end
155
-
156
159
  end
157
160
 
158
161
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb CHANGED
@@ -7,14 +7,17 @@ module BELParser
7
7
  module Language
8
8
  module Version2_0
9
9
  module Functions
10
- # MolecularActivity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale
10
+ # MolecularActivity: Denotes the frequency or abundance of events
11
+ # in which a member acts as a causal agent at the molecular scale
11
12
  class MolecularActivity
12
13
  extend Function
13
14
 
14
15
  SHORT = :ma
15
16
  LONG = :molecularActivity
16
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MolecularActivity
17
- DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale'.freeze
18
+ DESCRIPTION = 'Denotes the frequency or abundance of events
19
+ n which a member acts as a causal agent at the
20
+ olecular scale'.freeze
18
21
 
19
22
  def self.short
20
23
  SHORT
@@ -37,7 +40,7 @@ module BELParser
37
40
  end
38
41
 
39
42
  module Signatures
40
-
43
+ # MolecularActivitySignature
41
44
  class MolecularActivitySignature
42
45
  extend BELParser::Language::Signature
43
46
 
@@ -46,16 +49,16 @@ module BELParser
46
49
  # TODO: More constraints on prefix for activity namespace?
47
50
  AST = BELParser::Language::Semantics::Builder.build do
48
51
  term(
49
- function(
50
- identifier(
51
- function_of(MolecularActivity))),
52
- argument(
53
- parameter(
54
- prefix(any),
55
- value(
56
- value_type(
57
- has_encoding,
58
- encoding_of(:Activity))))))
52
+ function(
53
+ identifier(
54
+ function_of(MolecularActivity))),
55
+ argument(
56
+ parameter(
57
+ prefix(any),
58
+ value(
59
+ value_type(
60
+ has_encoding,
61
+ encoding_of(:Activity))))))
59
62
  end
60
63
  private_constant :AST
61
64
 
@@ -70,7 +73,6 @@ module BELParser
70
73
  STRING_FORM
71
74
  end
72
75
  end
73
-
74
76
  end
75
77
 
76
78
  SIGNATURES = Signatures.constants.map do |const|
data/lib/bel_parser/language/version2_0/functions/pathology.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # PathologySignature
41
41
  class PathologySignature
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(Pathology))),
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(:Pathology))))))
48
+ function(
49
+ identifier(
50
+ function_of(Pathology))),
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(:Pathology))))))
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|
data/lib/bel_parser/language/version2_0/functions/products.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ProductsSignature
41
41
  class ProductsSignature
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(Products))),
51
- variadic_arguments(
52
- term(
53
- function(
54
- identifier(
55
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
48
+ function(
49
+ identifier(
50
+ function_of(Products))),
51
+ variadic_arguments(
52
+ term(
53
+ function(
54
+ identifier(
55
+ return_type_of(BELParser::Language::Version2_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/version2_0/functions/protein_abundance.rb CHANGED
@@ -37,7 +37,7 @@ module BELParser
37
37
  end
38
38
 
39
39
  module Signatures
40
-
40
+ # ProteinAbundanceSignature
41
41
  class ProteinAbundanceSignature
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(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))))))
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
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
+ # ProteinAbundanceWithFragmentSignature
76
77
  class ProteinAbundanceWithFragmentSignature
77
78
  extend BELParser::Language::Signature
78
79
 
@@ -80,24 +81,24 @@ module BELParser
80
81
 
81
82
  AST = BELParser::Language::Semantics::Builder.build do
82
83
  term(
83
- function(
84
- identifier(
85
- function_of(ProteinAbundance))),
86
- argument(
87
- parameter(
88
- prefix(
89
- identifier(
90
- has_namespace,
91
- namespace_of(:*))),
92
- value(
93
- value_type(
94
- has_encoding,
95
- encoding_of(:ProteinAbundance))))),
96
- argument(
97
- term(
98
- function(
99
- identifier(
100
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fragment))))))
84
+ function(
85
+ identifier(
86
+ function_of(ProteinAbundance))),
87
+ argument(
88
+ parameter(
89
+ prefix(
90
+ identifier(
91
+ has_namespace,
92
+ namespace_of(:*))),
93
+ value(
94
+ value_type(
95
+ has_encoding,
96
+ encoding_of(:ProteinAbundance))))),
97
+ argument(
98
+ term(
99
+ function(
100
+ identifier(
101
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fragment))))))
101
102
  end
102
103
  private_constant :AST
103
104
 
@@ -112,7 +113,8 @@ module BELParser
112
113
  STRING_FORM
113
114
  end
114
115
  end
115
-
116
+
117
+ # ProteinAbundanceWithFusionSignature
116
118
  class ProteinAbundanceWithFusionSignature
117
119
  extend BELParser::Language::Signature
118
120
 
@@ -142,7 +144,8 @@ module BELParser
142
144
  STRING_FORM
143
145
  end
144
146
  end
145
-
147
+
148
+ # ProteinAbundanceWithLocationSignature
146
149
  class ProteinAbundanceWithLocationSignature
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(ProteinAbundance))),
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(:ProteinAbundance))))),
166
- argument(
167
- term(
168
- function(
169
- identifier(
170
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
156
+ function(
157
+ identifier(
158
+ function_of(ProteinAbundance))),
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(:ProteinAbundance))))),
169
+ argument(
170
+ term(
171
+ function(
172
+ identifier(
173
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
171
174
  end
172
175
  private_constant :AST
173
176
 
@@ -182,7 +185,8 @@ module BELParser
182
185
  STRING_FORM
183
186
  end
184
187
  end
185
-
188
+
189
+ # ProteinAbundanceWithProteinModificationSignature
186
190
  class ProteinAbundanceWithProteinModificationSignature
187
191
  extend BELParser::Language::Signature
188
192
 
@@ -190,24 +194,24 @@ module BELParser
190
194
 
191
195
  AST = BELParser::Language::Semantics::Builder.build do
192
196
  term(
193
- function(
194
- identifier(
195
- function_of(ProteinAbundance))),
196
- argument(
197
- parameter(
198
- prefix(
199
- identifier(
200
- has_namespace,
201
- namespace_of(:*))),
202
- value(
203
- value_type(
204
- has_encoding,
205
- encoding_of(:ProteinAbundance))))),
206
- variadic_arguments(
207
- term(
208
- function(
209
- identifier(
210
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::ProteinModification))))))
197
+ function(
198
+ identifier(
199
+ function_of(ProteinAbundance))),
200
+ argument(
201
+ parameter(
202
+ prefix(
203
+ identifier(
204
+ has_namespace,
205
+ namespace_of(:*))),
206
+ value(
207
+ value_type(
208
+ has_encoding,
209
+ encoding_of(:ProteinAbundance))))),
210
+ variadic_arguments(
211
+ term(
212
+ function(
213
+ identifier(
214
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::ProteinModification))))))
211
215
  end
212
216
  private_constant :AST
213
217
 
@@ -222,7 +226,8 @@ module BELParser
222
226
  STRING_FORM
223
227
  end
224
228
  end
225
-
229
+
230
+ # ProteinAbundanceWithVariantSignature
226
231
  class ProteinAbundanceWithVariantSignature
227
232
  extend BELParser::Language::Signature
228
233
 
@@ -230,24 +235,24 @@ module BELParser
230
235
 
231
236
  AST = BELParser::Language::Semantics::Builder.build do
232
237
  term(
233
- function(
234
- identifier(
235
- function_of(ProteinAbundance))),
236
- argument(
237
- parameter(
238
- prefix(
239
- identifier(
240
- has_namespace,
241
- namespace_of(:*))),
242
- value(
243
- value_type(
244
- has_encoding,
245
- encoding_of(:ProteinAbundance))))),
246
- argument(
247
- term(
248
- function(
249
- identifier(
250
- return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
238
+ function(
239
+ identifier(
240
+ function_of(ProteinAbundance))),
241
+ argument(
242
+ parameter(
243
+ prefix(
244
+ identifier(
245
+ has_namespace,
246
+ namespace_of(:*))),
247
+ value(
248
+ value_type(
249
+ has_encoding,
250
+ encoding_of(:ProteinAbundance))))),
251
+ argument(
252
+ term(
253
+ function(
254
+ identifier(
255
+ return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
251
256
  end
252
257
  private_constant :AST
253
258
 
@@ -262,7 +267,6 @@ module BELParser
262
267
  STRING_FORM
263
268
  end
264
269
  end
265
-
266
270
  end
267
271
 
268
272
  SIGNATURES = Signatures.constants.map do |const|