gff-nostream 3.0.9 → 3.0.10

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 (6) hide show
  1. package/dist/api.js +43 -30
  2. package/dist/api.js.map +1 -1
  3. package/esm/api.js +43 -30
  4. package/esm/api.js.map +1 -1
  5. package/package.json +1 -1
  6. package/src/api.ts +44 -29
package/dist/api.js CHANGED
@@ -13,6 +13,31 @@ function extractType(line) {
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  const t3 = line.indexOf('\t', t2 + 1);
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  return line.slice(t2 + 1, t3);
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  }
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+ /** Append a value to the array stored under key, creating the array if absent. */
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+ function appendOrphan(orphans, key, value) {
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+ const arr = orphans.get(key);
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+ if (arr) {
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+ arr.push(value);
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+ }
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+ else {
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+ orphans.set(key, [value]);
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+ }
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+ }
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+ /**
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+ * The JBrowse parser collapses single-element attribute arrays to scalars, so a
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+ * raw ID/Parent value can be a string, a string array, or absent. These coerce
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+ * those `unknown` values without typecasts.
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+ */
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+ function firstString(value) {
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+ const v = Array.isArray(value) ? value[0] : value;
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+ return typeof v === 'string' ? v : undefined;
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+ }
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+ function toStringArray(value) {
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+ if (Array.isArray(value)) {
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+ return value.filter((v) => typeof v === 'string');
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+ }
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+ return typeof value === 'string' ? [value] : [];
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+ }
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  /**
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  * Synchronously parse a string containing GFF3 and return an array of the
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  * parsed items.
@@ -120,12 +145,7 @@ function parseRecords(records) {
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  parent[0].child_features.push(feature);
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  }
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  else {
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- let arr = orphans.get(parentId);
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- if (!arr) {
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- arr = [];
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- orphans.set(parentId, arr);
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- }
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- arr.push(feature);
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+ appendOrphan(orphans, parentId, feature);
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  }
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  }
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  }
@@ -151,17 +171,18 @@ function parseRecordsJBrowse(records) {
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  if (record.lineHash !== undefined) {
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  feature._lineHash = String(record.lineHash);
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  }
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- // attribute parsing collapses single-element arrays to scalars, so id can
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- // be string | string[]; defensively take the first if multi-valued.
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- const rawId = feature.id;
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- const id = Array.isArray(rawId) ? rawId[0] : rawId;
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- const parent = feature.parent;
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- if (!id && !parent) {
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+ const id = firstString(feature.id);
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+ const parents = toStringArray(feature.parent);
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+ if (!id && parents.length === 0) {
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  items.push(feature);
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  }
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- else if (!id || !byId.has(id)) {
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- if (id) {
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- if (!parent) {
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+ else {
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+ // Register the id only the first time it is seen. Continuation lines
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+ // (multi-location features such as a CDS spanning several segments share
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+ // one ID across lines) skip registration but must still be attached to
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+ // their parent below, so this is independent of the parent handling.
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+ if (id && !byId.has(id)) {
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+ if (parents.length === 0) {
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  items.push(feature);
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  }
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  byId.set(id, feature);
@@ -173,21 +194,13 @@ function parseRecordsJBrowse(records) {
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  orphans.delete(id);
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  }
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  }
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- if (parent) {
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- const parents = Array.isArray(parent) ? parent : [parent];
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- for (const parentId of parents) {
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- const parentFeature = byId.get(parentId);
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- if (parentFeature) {
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- parentFeature.subfeatures.push(feature);
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- }
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- else {
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- let arr = orphans.get(parentId);
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- if (!arr) {
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- arr = [];
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- orphans.set(parentId, arr);
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- }
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- arr.push(feature);
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- }
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+ for (const parentId of parents) {
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+ const parentFeature = byId.get(parentId);
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+ if (parentFeature) {
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+ parentFeature.subfeatures.push(feature);
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+ }
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+ else {
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+ appendOrphan(orphans, parentId, feature);
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  }
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  }
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  }
package/dist/api.js.map CHANGED
@@ -1 +1 @@
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1
+ 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package/esm/api.js CHANGED
@@ -6,6 +6,31 @@ export function extractType(line) {
6
6
  const t3 = line.indexOf('\t', t2 + 1);
7
7
  return line.slice(t2 + 1, t3);
8
8
  }
9
+ /** Append a value to the array stored under key, creating the array if absent. */
10
+ function appendOrphan(orphans, key, value) {
11
+ const arr = orphans.get(key);
12
+ if (arr) {
13
+ arr.push(value);
14
+ }
15
+ else {
16
+ orphans.set(key, [value]);
17
+ }
18
+ }
19
+ /**
20
+ * The JBrowse parser collapses single-element attribute arrays to scalars, so a
21
+ * raw ID/Parent value can be a string, a string array, or absent. These coerce
22
+ * those `unknown` values without typecasts.
23
+ */
24
+ function firstString(value) {
25
+ const v = Array.isArray(value) ? value[0] : value;
26
+ return typeof v === 'string' ? v : undefined;
27
+ }
28
+ function toStringArray(value) {
29
+ if (Array.isArray(value)) {
30
+ return value.filter((v) => typeof v === 'string');
31
+ }
32
+ return typeof value === 'string' ? [value] : [];
33
+ }
9
34
  /**
10
35
  * Synchronously parse a string containing GFF3 and return an array of the
11
36
  * parsed items.
@@ -113,12 +138,7 @@ export function parseRecords(records) {
113
138
  parent[0].child_features.push(feature);
114
139
  }
115
140
  else {
116
- let arr = orphans.get(parentId);
117
- if (!arr) {
118
- arr = [];
119
- orphans.set(parentId, arr);
120
- }
121
- arr.push(feature);
141
+ appendOrphan(orphans, parentId, feature);
122
142
  }
123
143
  }
124
144
  }
@@ -144,17 +164,18 @@ export function parseRecordsJBrowse(records) {
144
164
  if (record.lineHash !== undefined) {
145
165
  feature._lineHash = String(record.lineHash);
146
166
  }
147
- // attribute parsing collapses single-element arrays to scalars, so id can
148
- // be string | string[]; defensively take the first if multi-valued.
149
- const rawId = feature.id;
150
- const id = Array.isArray(rawId) ? rawId[0] : rawId;
151
- const parent = feature.parent;
152
- if (!id && !parent) {
167
+ const id = firstString(feature.id);
168
+ const parents = toStringArray(feature.parent);
169
+ if (!id && parents.length === 0) {
153
170
  items.push(feature);
154
171
  }
155
- else if (!id || !byId.has(id)) {
156
- if (id) {
157
- if (!parent) {
172
+ else {
173
+ // Register the id only the first time it is seen. Continuation lines
174
+ // (multi-location features such as a CDS spanning several segments share
175
+ // one ID across lines) skip registration but must still be attached to
176
+ // their parent below, so this is independent of the parent handling.
177
+ if (id && !byId.has(id)) {
178
+ if (parents.length === 0) {
158
179
  items.push(feature);
159
180
  }
160
181
  byId.set(id, feature);
@@ -166,21 +187,13 @@ export function parseRecordsJBrowse(records) {
166
187
  orphans.delete(id);
167
188
  }
168
189
  }
169
- if (parent) {
170
- const parents = Array.isArray(parent) ? parent : [parent];
171
- for (const parentId of parents) {
172
- const parentFeature = byId.get(parentId);
173
- if (parentFeature) {
174
- parentFeature.subfeatures.push(feature);
175
- }
176
- else {
177
- let arr = orphans.get(parentId);
178
- if (!arr) {
179
- arr = [];
180
- orphans.set(parentId, arr);
181
- }
182
- arr.push(feature);
183
- }
190
+ for (const parentId of parents) {
191
+ const parentFeature = byId.get(parentId);
192
+ if (parentFeature) {
193
+ parentFeature.subfeatures.push(feature);
194
+ }
195
+ else {
196
+ appendOrphan(orphans, parentId, feature);
184
197
  }
185
198
  }
186
199
  }
package/esm/api.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "gff-nostream",
3
- "version": "3.0.9",
3
+ "version": "3.0.10",
4
4
  "description": "utilities to read GFF3 data",
5
5
  "license": "MIT",
6
6
  "repository": {
package/src/api.ts CHANGED
@@ -34,6 +34,33 @@ export function extractType(line: string): string {
34
34
  return line.slice(t2 + 1, t3)
35
35
  }
36
36
 
37
+ /** Append a value to the array stored under key, creating the array if absent. */
38
+ function appendOrphan<T>(orphans: Map<string, T[]>, key: string, value: T) {
39
+ const arr = orphans.get(key)
40
+ if (arr) {
41
+ arr.push(value)
42
+ } else {
43
+ orphans.set(key, [value])
44
+ }
45
+ }
46
+
47
+ /**
48
+ * The JBrowse parser collapses single-element attribute arrays to scalars, so a
49
+ * raw ID/Parent value can be a string, a string array, or absent. These coerce
50
+ * those `unknown` values without typecasts.
51
+ */
52
+ function firstString(value: unknown): string | undefined {
53
+ const v: unknown = Array.isArray(value) ? value[0] : value
54
+ return typeof v === 'string' ? v : undefined
55
+ }
56
+
57
+ function toStringArray(value: unknown): string[] {
58
+ if (Array.isArray(value)) {
59
+ return value.filter((v): v is string => typeof v === 'string')
60
+ }
61
+ return typeof value === 'string' ? [value] : []
62
+ }
63
+
37
64
  /**
38
65
  * Synchronously parse a string containing GFF3 and return an array of the
39
66
  * parsed items.
@@ -145,12 +172,7 @@ export function parseRecords(records: ParseInput[]): GFF3Feature[] {
145
172
  // so push once via the first line.
146
173
  parent[0]!.child_features.push(feature)
147
174
  } else {
148
- let arr = orphans.get(parentId)
149
- if (!arr) {
150
- arr = []
151
- orphans.set(parentId, arr)
152
- }
153
- arr.push(feature)
175
+ appendOrphan(orphans, parentId, feature)
154
176
  }
155
177
  }
156
178
  }
@@ -181,17 +203,18 @@ export function parseRecordsJBrowse(records: ParseInput[]): JBrowseFeature[] {
181
203
  feature._lineHash = String(record.lineHash)
182
204
  }
183
205
 
184
- // attribute parsing collapses single-element arrays to scalars, so id can
185
- // be string | string[]; defensively take the first if multi-valued.
186
- const rawId = feature.id as string | string[] | undefined
187
- const id = Array.isArray(rawId) ? rawId[0] : rawId
188
- const parent = feature.parent as string | string[] | undefined
206
+ const id = firstString(feature.id)
207
+ const parents = toStringArray(feature.parent)
189
208
 
190
- if (!id && !parent) {
209
+ if (!id && parents.length === 0) {
191
210
  items.push(feature)
192
- } else if (!id || !byId.has(id)) {
193
- if (id) {
194
- if (!parent) {
211
+ } else {
212
+ // Register the id only the first time it is seen. Continuation lines
213
+ // (multi-location features such as a CDS spanning several segments share
214
+ // one ID across lines) skip registration but must still be attached to
215
+ // their parent below, so this is independent of the parent handling.
216
+ if (id && !byId.has(id)) {
217
+ if (parents.length === 0) {
195
218
  items.push(feature)
196
219
  }
197
220
  byId.set(id, feature)
@@ -204,20 +227,12 @@ export function parseRecordsJBrowse(records: ParseInput[]): JBrowseFeature[] {
204
227
  }
205
228
  }
206
229
 
207
- if (parent) {
208
- const parents = Array.isArray(parent) ? parent : [parent]
209
- for (const parentId of parents) {
210
- const parentFeature = byId.get(parentId)
211
- if (parentFeature) {
212
- parentFeature.subfeatures.push(feature)
213
- } else {
214
- let arr = orphans.get(parentId)
215
- if (!arr) {
216
- arr = []
217
- orphans.set(parentId, arr)
218
- }
219
- arr.push(feature)
220
- }
230
+ for (const parentId of parents) {
231
+ const parentFeature = byId.get(parentId)
232
+ if (parentFeature) {
233
+ parentFeature.subfeatures.push(feature)
234
+ } else {
235
+ appendOrphan(orphans, parentId, feature)
221
236
  }
222
237
  }
223
238
  }