@graphty/graph-io 0.3.25 → 0.3.27

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 (581) hide show
  1. package/README.md +49 -414
  2. package/dist/chunks/children-CL3Cy0ez.js.map +1 -1
  3. package/dist/chunks/choose-DrXtu_96.js +56 -0
  4. package/dist/chunks/choose-DrXtu_96.js.map +1 -0
  5. package/dist/chunks/constants-ikG85dT8.js +231 -0
  6. package/dist/chunks/constants-ikG85dT8.js.map +1 -0
  7. package/dist/chunks/{escape-B-tkk_Cl.js → escape-D1HPTUrP.js} +390 -99
  8. package/dist/chunks/escape-D1HPTUrP.js.map +1 -0
  9. package/dist/chunks/export-CHd4tQE2.js +4333 -0
  10. package/dist/chunks/export-CHd4tQE2.js.map +1 -0
  11. package/dist/chunks/{importer-eUREhBGj.js → exporter-D23CKNqF.js} +4969 -3201
  12. package/dist/chunks/exporter-D23CKNqF.js.map +1 -0
  13. package/dist/chunks/{exporter-DIeGJXAZ.js → exporter-DfWTgrti.js} +23 -21
  14. package/dist/chunks/exporter-DfWTgrti.js.map +1 -0
  15. package/dist/chunks/exporter-DhtW6FxK.js +3465 -0
  16. package/dist/chunks/exporter-DhtW6FxK.js.map +1 -0
  17. package/dist/chunks/{exporter-BGrsWamJ.js → exporter-IHv4nkCm.js} +38 -229
  18. package/dist/chunks/exporter-IHv4nkCm.js.map +1 -0
  19. package/dist/chunks/{importer-BWY2FFc5.js → importer-B1wmPQjr.js} +255 -77
  20. package/dist/chunks/importer-B1wmPQjr.js.map +1 -0
  21. package/dist/chunks/{importer-D_e7e7LX.js → importer-B2W_58pz.js} +399 -146
  22. package/dist/chunks/importer-B2W_58pz.js.map +1 -0
  23. package/dist/chunks/importer-BSALvkui.js +2811 -0
  24. package/dist/chunks/importer-BSALvkui.js.map +1 -0
  25. package/dist/chunks/{importer-vi3bSdtw.js → importer-BVRE--Un.js} +510 -77
  26. package/dist/chunks/importer-BVRE--Un.js.map +1 -0
  27. package/dist/chunks/{importer-DET1tg6s.js → importer-CIAzt-wo.js} +1689 -312
  28. package/dist/chunks/importer-CIAzt-wo.js.map +1 -0
  29. package/dist/chunks/{importer-DIrbbnAf.js → importer-DpEW5zeG.js} +585 -226
  30. package/dist/chunks/importer-DpEW5zeG.js.map +1 -0
  31. package/dist/chunks/{importer-zGLo8Dg_.js → importer-z_FL4VMb.js} +488 -161
  32. package/dist/chunks/importer-z_FL4VMb.js.map +1 -0
  33. package/dist/chunks/json-elements-BAmNBZok.js +1225 -0
  34. package/dist/chunks/json-elements-BAmNBZok.js.map +1 -0
  35. package/dist/chunks/ontology-export-Bab4eUA8.js +357 -0
  36. package/dist/chunks/ontology-export-Bab4eUA8.js.map +1 -0
  37. package/dist/chunks/{records-dbRkxwaq.js → records-CdlvL4RO.js} +298 -114
  38. package/dist/chunks/records-CdlvL4RO.js.map +1 -0
  39. package/dist/chunks/{text-Dr0Ifpag.js → text-DzXjAiTl.js} +29 -11
  40. package/dist/chunks/text-DzXjAiTl.js.map +1 -0
  41. package/dist/chunks/{writer-C7flM-Ih.js → writer-DxjgHwSe.js} +19 -1
  42. package/dist/chunks/writer-DxjgHwSe.js.map +1 -0
  43. package/dist/csv.js +952 -262
  44. package/dist/csv.js.map +1 -1
  45. package/dist/cx.js +6 -3
  46. package/dist/cx2.js +2 -2
  47. package/dist/cys.js +6 -3
  48. package/dist/dot.js +1 -1
  49. package/dist/gexf.js +554 -122
  50. package/dist/gexf.js.map +1 -1
  51. package/dist/gml.js +344 -87
  52. package/dist/gml.js.map +1 -1
  53. package/dist/graph-io.js +1105 -213
  54. package/dist/graph-io.js.map +1 -1
  55. package/dist/graphml.js +3 -2
  56. package/dist/graphml.js.map +1 -1
  57. package/dist/json.js +3 -2
  58. package/dist/neo4j.js +565 -158
  59. package/dist/neo4j.js.map +1 -1
  60. package/dist/obo.js +6 -3
  61. package/dist/pajek.js +1 -1
  62. package/dist/src/children.d.ts +18 -6
  63. package/dist/src/children.d.ts.map +1 -1
  64. package/dist/src/children.js +6 -3
  65. package/dist/src/children.js.map +1 -1
  66. package/dist/src/common/attributes.d.ts +29 -11
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  68. package/dist/src/common/attributes.js +25 -7
  69. package/dist/src/common/attributes.js.map +1 -1
  70. package/dist/src/common/cell-budget.d.ts +9 -2
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  72. package/dist/src/common/cell-budget.js +11 -3
  73. package/dist/src/common/cell-budget.js.map +1 -1
  74. package/dist/src/common/choose.d.ts +19 -0
  75. package/dist/src/common/choose.d.ts.map +1 -0
  76. package/dist/src/common/choose.js +72 -0
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  78. package/dist/src/common/codes.d.ts +456 -66
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  80. package/dist/src/common/codes.js +458 -66
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  82. package/dist/src/common/compare.d.ts +81 -0
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  84. package/dist/src/common/compare.js +394 -0
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  86. package/dist/src/common/cx-export.d.ts +123 -0
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  88. package/dist/src/common/cx-export.js +334 -0
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  90. package/dist/src/common/declared-types.d.ts +22 -2
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  94. package/dist/src/common/direction.d.ts +74 -50
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  96. package/dist/src/common/direction.js +47 -27
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  98. package/dist/src/common/escape.d.ts +21 -9
  99. package/dist/src/common/escape.d.ts.map +1 -1
  100. package/dist/src/common/escape.js +39 -22
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  102. package/dist/src/common/export.d.ts +144 -32
  103. package/dist/src/common/export.d.ts.map +1 -1
  104. package/dist/src/common/export.js +216 -42
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  106. package/dist/src/common/format.d.ts +23 -1
  107. package/dist/src/common/format.d.ts.map +1 -1
  108. package/dist/src/common/format.js +26 -1
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  110. package/dist/src/common/ids.d.ts +9 -2
  111. package/dist/src/common/ids.d.ts.map +1 -1
  112. package/dist/src/common/ids.js +6 -2
  113. package/dist/src/common/ids.js.map +1 -1
  114. package/dist/src/common/input.d.ts +122 -28
  115. package/dist/src/common/input.d.ts.map +1 -1
  116. package/dist/src/common/input.js +890 -124
  117. package/dist/src/common/input.js.map +1 -1
  118. package/dist/src/common/json-elements.d.ts +144 -20
  119. package/dist/src/common/json-elements.d.ts.map +1 -1
  120. package/dist/src/common/json-elements.js +869 -189
  121. package/dist/src/common/json-elements.js.map +1 -1
  122. package/dist/src/common/line-format.d.ts +90 -0
  123. package/dist/src/common/line-format.d.ts.map +1 -0
  124. package/dist/src/common/line-format.js +185 -0
  125. package/dist/src/common/line-format.js.map +1 -0
  126. package/dist/src/common/lists.d.ts +6 -1
  127. package/dist/src/common/lists.d.ts.map +1 -1
  128. package/dist/src/common/lists.js +3 -1
  129. package/dist/src/common/lists.js.map +1 -1
  130. package/dist/src/common/ontology-export.d.ts +167 -0
  131. package/dist/src/common/ontology-export.d.ts.map +1 -0
  132. package/dist/src/common/ontology-export.js +359 -0
  133. package/dist/src/common/ontology-export.js.map +1 -0
  134. package/dist/src/common/ontology.d.ts +25 -3
  135. package/dist/src/common/ontology.d.ts.map +1 -1
  136. package/dist/src/common/ontology.js +30 -9
  137. package/dist/src/common/ontology.js.map +1 -1
  138. package/dist/src/common/options.d.ts +62 -12
  139. package/dist/src/common/options.d.ts.map +1 -1
  140. package/dist/src/common/options.js +89 -11
  141. package/dist/src/common/options.js.map +1 -1
  142. package/dist/src/common/plural.d.ts +31 -0
  143. package/dist/src/common/plural.d.ts.map +1 -0
  144. package/dist/src/common/plural.js +46 -0
  145. package/dist/src/common/plural.js.map +1 -0
  146. package/dist/src/common/report.d.ts +72 -14
  147. package/dist/src/common/report.d.ts.map +1 -1
  148. package/dist/src/common/report.js +146 -22
  149. package/dist/src/common/report.js.map +1 -1
  150. package/dist/src/common/temporal.d.ts +22 -5
  151. package/dist/src/common/temporal.d.ts.map +1 -1
  152. package/dist/src/common/temporal.js +13 -2
  153. package/dist/src/common/temporal.js.map +1 -1
  154. package/dist/src/common/text.d.ts +39 -23
  155. package/dist/src/common/text.d.ts.map +1 -1
  156. package/dist/src/common/text.js +51 -21
  157. package/dist/src/common/text.js.map +1 -1
  158. package/dist/src/common/weights.d.ts +37 -4
  159. package/dist/src/common/weights.d.ts.map +1 -1
  160. package/dist/src/common/weights.js +61 -2
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  162. package/dist/src/common/writer.d.ts +19 -3
  163. package/dist/src/common/writer.d.ts.map +1 -1
  164. package/dist/src/common/writer.js +30 -2
  165. package/dist/src/common/writer.js.map +1 -1
  166. package/dist/src/common/xml.d.ts +125 -9
  167. package/dist/src/common/xml.d.ts.map +1 -1
  168. package/dist/src/common/xml.js +402 -85
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  170. package/dist/src/common/zip.d.ts +44 -4
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  172. package/dist/src/common/zip.js +134 -5
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  174. package/dist/src/formats/csv/exporter.d.ts +80 -24
  175. package/dist/src/formats/csv/exporter.d.ts.map +1 -1
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  178. package/dist/src/formats/csv/header.d.ts +38 -9
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  190. package/dist/src/formats/csv/records.d.ts +95 -10
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1
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package/dist/src/formats/obo/index.d.ts CHANGED
@@ -1,7 +1,10 @@
1
1
  /**
2
- * The OBO subpath entry (`@graphty/graph-io/obo`, design section 1.5): the importer of the OBO
3
- * flat file format (the Gene Ontology and the OBO Foundry ontologies), its options and its issue
4
- * codes. OBO is read-only: there is no exporter.
2
+ * The OBO subpath entry (`@graphty/graph-io/obo`): the importer and exporter of the OBO flat file
3
+ * format (the Gene Ontology and the OBO Foundry ontologies), their options and their issue and
4
+ * loss codes. The JSON form of the same ontologies, OBO Graphs, is the `obographs` dialect of
5
+ * `@graphty/graph-io/json`.
6
+ * @module @graphty/graph-io/obo
5
7
  */
8
+ export { OBO_CAPABILITIES, OBO_LOSS, oboExporter, type OboExportOptions } from "./exporter.js";
6
9
  export { OBO_ISSUE, oboImporter, type OboImportOptions } from "./importer.js";
7
10
  //# sourceMappingURL=index.d.ts.map
package/dist/src/formats/obo/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/formats/obo/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,KAAK,gBAAgB,EAAE,MAAM,eAAe,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/formats/obo/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAC/F,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,KAAK,gBAAgB,EAAE,MAAM,eAAe,CAAC"}
package/dist/src/formats/obo/index.js CHANGED
@@ -1,7 +1,10 @@
1
1
  /**
2
- * The OBO subpath entry (`@graphty/graph-io/obo`, design section 1.5): the importer of the OBO
3
- * flat file format (the Gene Ontology and the OBO Foundry ontologies), its options and its issue
4
- * codes. OBO is read-only: there is no exporter.
2
+ * The OBO subpath entry (`@graphty/graph-io/obo`): the importer and exporter of the OBO flat file
3
+ * format (the Gene Ontology and the OBO Foundry ontologies), their options and their issue and
4
+ * loss codes. The JSON form of the same ontologies, OBO Graphs, is the `obographs` dialect of
5
+ * `@graphty/graph-io/json`.
6
+ * @module @graphty/graph-io/obo
5
7
  */
8
+ export { OBO_CAPABILITIES, OBO_LOSS, oboExporter } from "./exporter.js";
6
9
  export { OBO_ISSUE, oboImporter } from "./importer.js";
7
10
  //# sourceMappingURL=index.js.map
package/dist/src/formats/obo/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/formats/obo/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,WAAW,EAAyB,MAAM,eAAe,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/formats/obo/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,WAAW,EAAyB,MAAM,eAAe,CAAC;AAC/F,OAAO,EAAE,SAAS,EAAE,WAAW,EAAyB,MAAM,eAAe,CAAC"}
package/dist/src/formats/obo/syntax.d.ts CHANGED
@@ -12,12 +12,22 @@
12
12
  * backslash at the very end is dropped.
13
13
  * @param text - raw text
14
14
  * @returns the unescaped text
15
+ * @category Plugin helpers
15
16
  */
16
17
  export declare function unescapeObo(text: string): string;
18
+ /**
19
+ * Split a line at the form feeds outside quotes (the 1.4 grammar counts a form feed as a line end;
20
+ * one inside a quoted value is text).
21
+ * @param line - the raw line
22
+ * @returns the pieces, the line itself when it holds no such form feed
23
+ * @category Plugin helpers
24
+ */
25
+ export declare function splitFormFeeds(line: string): string[];
17
26
  /**
18
27
  * Whether a raw line ends with an unescaped backslash (the 1.0 / 1.2 line continuation).
19
28
  * @param line - the raw line, trailing whitespace included
20
29
  * @returns true when the line continues on the next one
30
+ * @category Plugin helpers
21
31
  */
22
32
  export declare function endsWithContinuation(line: string): boolean;
23
33
  /** A tag-value line split at its first unescaped colon. */
@@ -31,6 +41,7 @@ interface TagValue {
31
41
  * Split a line at its first unescaped colon (values contain colons freely: `is_a: GO:0000001`).
32
42
  * @param line - the raw line, trimmed
33
43
  * @returns the tag and the rest, or null when the line has no colon
44
+ * @category Plugin helpers
34
45
  */
35
46
  export declare function splitTagValue(line: string): TagValue | null;
36
47
  /**
@@ -41,9 +52,13 @@ export declare function splitTagValue(line: string): TagValue | null;
41
52
  * hide the comment after it.
42
53
  * @param rest - the raw value
43
54
  * @returns the value before the comment, trailing whitespace removed
55
+ * @category Plugin helpers
44
56
  */
45
57
  export declare function stripComment(rest: string): string;
46
- /** The qualifiers of a clause: name to value (a list when a name repeats). */
58
+ /**
59
+ * The qualifiers of a clause: name to value (a list when a name repeats).
60
+ * @category Plugin helpers
61
+ */
47
62
  export type Qualifiers = Record<string, string | string[]>;
48
63
  /** A value with its trailing qualifier blocks split off. */
49
64
  interface QualifiedValue {
@@ -57,20 +72,34 @@ interface QualifiedValue {
57
72
  /**
58
73
  * Split the trailing qualifier blocks off a value: a `{...}` is a block only when it closes the
59
74
  * value (after the comment was stripped); several blocks (`{a="1"}{b="2"}`, 1.2 examples) are
60
- * merged. A closing brace whose block does not parse is left in the value and reported.
75
+ * merged. A closing brace whose block does not parse is left in the value and reported. The value
76
+ * is scanned once, so a value of many blocks costs its length, not its length times its blocks.
61
77
  * @param value - the raw value without its comment
62
78
  * @returns the value and its qualifiers
79
+ * @category Plugin helpers
63
80
  */
64
81
  export declare function splitQualifiers(value: string): QualifiedValue;
82
+ /**
83
+ * The index of an unescaped `{` outside quotes that no `}` closes: a qualifier block cut short (a
84
+ * file truncated inside it).
85
+ * @param value - a raw value, closing blocks already split off
86
+ * @returns the index, or -1 when every brace is closed
87
+ * @category Plugin helpers
88
+ */
89
+ export declare function unclosedBlock(value: string): number;
65
90
  /**
66
91
  * Parse the inside of a qualifier block: `name="value"` pairs separated by commas, the 1.2
67
92
  * unquoted form (`source=PMID:1`) and missing spaces accepted. A name is everything up to `=`
68
93
  * (qualifier names may be IRIs with colons).
69
94
  * @param inner - the text between the braces
70
95
  * @returns the qualifiers, or null when the block does not parse (a pair without `=`, an unclosed quote)
96
+ * @category Plugin helpers
71
97
  */
72
98
  export declare function parseQualifiers(inner: string): Qualifiers | null;
73
- /** One token of a value. */
99
+ /**
100
+ * One token of a value.
101
+ * @category Plugin helpers
102
+ */
74
103
  export interface Token {
75
104
  /** A bare word, a quoted string or a bracketed list. */
76
105
  readonly kind: "word" | "quoted" | "list";
@@ -84,9 +113,13 @@ export interface Token {
84
113
  * Whitespace separates tokens; an escaped space belongs to its word.
85
114
  * @param value - the raw value
86
115
  * @returns the tokens
116
+ * @category Plugin helpers
87
117
  */
88
118
  export declare function tokenize(value: string): Token[];
89
- /** One cross-reference: `ID "description" {qualifiers}`. */
119
+ /**
120
+ * One cross-reference: `ID "description" {qualifiers}`.
121
+ * @category Plugin helpers
122
+ */
90
123
  export interface Xref {
91
124
  /** The id (may hold spaces: `NIST Chemistry WebBook:110-63-4`, which owlapi reads). */
92
125
  readonly id: string;
@@ -94,12 +127,15 @@ export interface Xref {
94
127
  readonly description: string | null;
95
128
  /** Per-xref qualifiers (OBO 1.2 inside a list), or null. */
96
129
  readonly qualifiers: Qualifiers | null;
130
+ /** Whether the description's quote was never closed (it runs to the end). */
131
+ readonly unterminated: boolean;
97
132
  }
98
133
  /**
99
134
  * Read one cross-reference: the id is the text before the first unescaped quote, the quoted
100
135
  * string its description, a closing block its qualifiers.
101
136
  * @param raw - the raw text of one xref
102
137
  * @returns the xref, or null when it has no id
138
+ * @category Plugin helpers
103
139
  */
104
140
  export declare function parseXref(raw: string): Xref | null;
105
141
  /**
@@ -107,6 +143,7 @@ export declare function parseXref(raw: string): Xref | null;
107
143
  * braces (a solitary xref needs no escaping of its commas only outside a list).
108
144
  * @param inner - the raw text between the brackets
109
145
  * @returns the xrefs, in order
146
+ * @category Plugin helpers
110
147
  */
111
148
  export declare function parseXrefList(inner: string): Xref[];
112
149
  /**
@@ -115,7 +152,74 @@ export declare function parseXrefList(inner: string): Xref[];
115
152
  * have escaped).
116
153
  * @param value - the raw value, qualifiers already split off
117
154
  * @returns true when a stray brace is present
155
+ * @category Plugin helpers
118
156
  */
119
157
  export declare function hasStrayBrace(value: string): boolean;
158
+ /**
159
+ * Whether a text holds a carriage return or a form feed, which the OBO line grammar reads as a line
160
+ * end wherever it stands and no escape can spell; the writers turn them into `\n`.
161
+ * @param text - the text
162
+ * @returns true when the text loses a character on the way through an OBO file
163
+ * @category Plugin helpers
164
+ */
165
+ export declare function hasLineEnd(text: string): boolean;
166
+ /**
167
+ * Escape text for a quoted OBO string (`def: "..."`, a synonym, a qualifier value): backslash,
168
+ * quote, newline and tab. A carriage return or form feed becomes a newline (see hasLineEnd()).
169
+ * `\W` is never written: graph-io reads it as a space, fastobo and the 1.4 BNF as the letter W.
170
+ * @param text - the text
171
+ * @returns the escaped text, without the quotes
172
+ * @category Plugin helpers
173
+ */
174
+ export declare function escapeOboQuoted(text: string): string;
175
+ /**
176
+ * Escape text for an unquoted OBO value (`name:`, `comment:`, an xref id, an unknown tag): what
177
+ * escapeOboQuoted() escapes plus `!` (a comment), `{` and `}` (a qualifier block), `[`, `]` and `,`
178
+ * (an xref list) and `"` (a quoted string). The reader trims an unquoted value, so its leading
179
+ * and trailing spaces cannot be kept.
180
+ * @param text - the text
181
+ * @returns the escaped text
182
+ * @category Plugin helpers
183
+ */
184
+ export declare function escapeOboValue(text: string): string;
185
+ /**
186
+ * Whether a text can stand as one OBO word (an id, a relation, a subset or synonym type name): not
187
+ * empty, no whitespace, no control character (the importer refuses an id holding one), no `!`, `{`
188
+ * or `}`. escapeOboWord() escapes what else would end it or turn
189
+ * it into another token (a backslash, a quote, a leading `[`).
190
+ * @param text - the text
191
+ * @returns true when the text is a word
192
+ * @category Plugin helpers
193
+ */
194
+ export declare function isOboWord(text: string): boolean;
195
+ /**
196
+ * A character an OBO word cannot hold: whitespace, a control character, `!`, `{` or `}`.
197
+ * @category Plugin helpers
198
+ */
199
+ export declare const NOT_IN_WORD: RegExp;
200
+ /**
201
+ * Write a word (see isOboWord()): a backslash and a quote escaped, and a leading `[` (which would
202
+ * open an xref list).
203
+ * @param word - a text isOboWord() accepts
204
+ * @returns the text to write
205
+ * @category Plugin helpers
206
+ */
207
+ export declare function escapeOboWord(word: string): string;
208
+ /**
209
+ * Whether a text can be a qualifier name: not empty, no surrounding space, none of `=`, `"`, `,`,
210
+ * `{`, `}`, `[`, `]`, `!`, a backslash or a line end (the reader takes a name as everything up to
211
+ * the first `=`, unescaped only after the split).
212
+ * @param name - the name
213
+ * @returns true when the name is written as it is
214
+ * @category Plugin helpers
215
+ */
216
+ export declare function isQualifierName(name: string): boolean;
217
+ /**
218
+ * A qualifier block: `{name="value", ...}`, a list value as one pair per item.
219
+ * @param pairs - the name / value pairs, in order (names isQualifierName() accepts)
220
+ * @returns the block with a leading space, or "" when there are no pairs
221
+ * @category Plugin helpers
222
+ */
223
+ export declare function qualifierBlock(pairs: readonly (readonly [string, string])[]): string;
120
224
  export {};
121
225
  //# sourceMappingURL=syntax.d.ts.map
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