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/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|