@genome-spy/core 0.36.1 → 0.37.0

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 (523) hide show
  1. package/README.md +1 -0
  2. package/dist/{index.es.js → bundled/index.es.js} +2253 -2115
  3. package/dist/{index.js → bundled/index.js} +180 -44
  4. package/dist/src/data/collector.d.ts +36 -0
  5. package/dist/src/data/collector.d.ts.map +1 -0
  6. package/dist/src/data/collector.js +184 -0
  7. package/dist/src/data/collector.test.js +84 -0
  8. package/dist/src/data/dataFlow.d.ts +65 -0
  9. package/dist/src/data/dataFlow.d.ts.map +1 -0
  10. package/dist/src/data/dataFlow.js +142 -0
  11. package/dist/src/data/dataFlow.test.js +5 -0
  12. package/dist/src/data/facetNode.d.ts +17 -0
  13. package/dist/src/data/facetNode.d.ts.map +1 -0
  14. package/dist/src/data/facetNode.js +17 -0
  15. package/dist/src/data/flow.test.js +72 -0
  16. package/dist/src/data/flowNode.d.ts +136 -0
  17. package/dist/src/data/flowNode.d.ts.map +1 -0
  18. package/dist/src/data/flowNode.js +286 -0
  19. package/dist/src/data/flowNode.test.js +50 -0
  20. package/dist/src/data/flowOptimizer.d.ts +27 -0
  21. package/dist/src/data/flowOptimizer.d.ts.map +1 -0
  22. package/dist/src/data/flowOptimizer.js +133 -0
  23. package/dist/src/data/flowOptimizer.test.js +193 -0
  24. package/dist/src/data/flowTestUtils.d.ts +30 -0
  25. package/dist/src/data/flowTestUtils.d.ts.map +1 -0
  26. package/dist/src/data/flowTestUtils.js +63 -0
  27. package/dist/src/data/formats/fasta.d.ts +20 -0
  28. package/dist/src/data/formats/fasta.d.ts.map +1 -0
  29. package/dist/src/data/formats/fasta.js +32 -0
  30. package/dist/src/data/formats/fasta.test.js +27 -0
  31. package/dist/src/data/sources/dataSource.d.ts +12 -0
  32. package/dist/src/data/sources/dataSource.d.ts.map +1 -0
  33. package/dist/src/data/sources/dataSource.js +25 -0
  34. package/dist/src/data/sources/dataSourceFactory.d.ts +16 -0
  35. package/dist/src/data/sources/dataSourceFactory.d.ts.map +1 -0
  36. package/dist/src/data/sources/dataSourceFactory.js +127 -0
  37. package/dist/src/data/sources/dataUtils.d.ts +50 -0
  38. package/dist/src/data/sources/dataUtils.d.ts.map +1 -0
  39. package/dist/src/data/sources/dataUtils.js +83 -0
  40. package/dist/src/data/sources/dynamic/README.md +3 -0
  41. package/dist/src/data/sources/dynamic/axisGenomeSource.d.ts +13 -0
  42. package/dist/src/data/sources/dynamic/axisGenomeSource.d.ts.map +1 -0
  43. package/dist/src/data/sources/dynamic/axisGenomeSource.js +19 -0
  44. package/dist/src/data/sources/dynamic/axisTickSource.d.ts +18 -0
  45. package/dist/src/data/sources/dynamic/axisTickSource.d.ts.map +1 -0
  46. package/dist/src/data/sources/dynamic/axisTickSource.js +73 -0
  47. package/dist/src/data/sources/dynamic/bamSource.d.ts +46 -0
  48. package/dist/src/data/sources/dynamic/bamSource.d.ts.map +1 -0
  49. package/dist/src/data/sources/dynamic/bamSource.js +115 -0
  50. package/dist/src/data/sources/dynamic/bigBedSource.d.ts +51 -0
  51. package/dist/src/data/sources/dynamic/bigBedSource.d.ts.map +1 -0
  52. package/dist/src/data/sources/dynamic/bigBedSource.js +128 -0
  53. package/dist/src/data/sources/dynamic/bigWigSource.d.ts +58 -0
  54. package/dist/src/data/sources/dynamic/bigWigSource.d.ts.map +1 -0
  55. package/dist/src/data/sources/dynamic/bigWigSource.js +166 -0
  56. package/dist/src/data/sources/dynamic/gff3Source.d.ts +8 -0
  57. package/dist/src/data/sources/dynamic/gff3Source.d.ts.map +1 -0
  58. package/dist/src/data/sources/dynamic/gff3Source.js +19 -0
  59. package/dist/src/data/sources/dynamic/indexedFastaSource.d.ts +30 -0
  60. package/dist/src/data/sources/dynamic/indexedFastaSource.d.ts.map +1 -0
  61. package/dist/src/data/sources/dynamic/indexedFastaSource.js +86 -0
  62. package/dist/src/data/sources/dynamic/singleAxisLazySource.d.ts +42 -0
  63. package/dist/src/data/sources/dynamic/singleAxisLazySource.d.ts.map +1 -0
  64. package/dist/src/data/sources/dynamic/singleAxisLazySource.js +129 -0
  65. package/dist/src/data/sources/dynamic/tabixSource.d.ts +54 -0
  66. package/dist/src/data/sources/dynamic/tabixSource.d.ts.map +1 -0
  67. package/dist/src/data/sources/dynamic/tabixSource.js +140 -0
  68. package/dist/src/data/sources/dynamic/windowedMixin.d.ts +32 -0
  69. package/dist/src/data/sources/dynamic/windowedMixin.d.ts.map +1 -0
  70. package/dist/src/data/sources/dynamic/windowedMixin.js +53 -0
  71. package/dist/src/data/sources/inlineSource.d.ts +16 -0
  72. package/dist/src/data/sources/inlineSource.d.ts.map +1 -0
  73. package/dist/src/data/sources/inlineSource.js +68 -0
  74. package/dist/src/data/sources/inlineSource.test.js +56 -0
  75. package/dist/src/data/sources/namedSource.d.ts +25 -0
  76. package/dist/src/data/sources/namedSource.d.ts.map +1 -0
  77. package/dist/src/data/sources/namedSource.js +80 -0
  78. package/dist/src/data/sources/sequenceSource.d.ts +17 -0
  79. package/dist/src/data/sources/sequenceSource.d.ts.map +1 -0
  80. package/dist/src/data/sources/sequenceSource.js +47 -0
  81. package/dist/src/data/sources/sequenceSource.test.js +46 -0
  82. package/dist/src/data/sources/urlSource.d.ts +16 -0
  83. package/dist/src/data/sources/urlSource.d.ts.map +1 -0
  84. package/dist/src/data/sources/urlSource.js +74 -0
  85. package/dist/src/data/transforms/aggregate.d.ts +18 -0
  86. package/dist/src/data/transforms/aggregate.d.ts.map +1 -0
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  88. package/dist/src/data/transforms/clone.d.ts +15 -0
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  92. package/dist/src/data/transforms/coverage.d.ts +30 -0
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  95. package/dist/src/data/transforms/coverage.test.js +123 -0
  96. package/dist/src/data/transforms/filter.d.ts +12 -0
  97. package/dist/src/data/transforms/filter.d.ts.map +1 -0
  98. package/dist/src/data/transforms/filter.js +33 -0
  99. package/dist/src/data/transforms/filter.test.js +18 -0
  100. package/dist/src/data/transforms/filterScoredLabels.d.ts +29 -0
  101. package/dist/src/data/transforms/filterScoredLabels.d.ts.map +1 -0
  102. package/dist/src/data/transforms/filterScoredLabels.js +134 -0
  103. package/dist/src/data/transforms/flatten.d.ts +10 -0
  104. package/dist/src/data/transforms/flatten.d.ts.map +1 -0
  105. package/dist/src/data/transforms/flatten.js +68 -0
  106. package/dist/src/data/transforms/flatten.test.js +93 -0
  107. package/dist/src/data/transforms/flattenCompressedExons.d.ts +19 -0
  108. package/dist/src/data/transforms/flattenCompressedExons.d.ts.map +1 -0
  109. package/dist/src/data/transforms/flattenCompressedExons.js +53 -0
  110. package/dist/src/data/transforms/flattenDelimited.d.ts +10 -0
  111. package/dist/src/data/transforms/flattenDelimited.d.ts.map +1 -0
  112. package/dist/src/data/transforms/flattenDelimited.js +66 -0
  113. package/dist/src/data/transforms/flattenDelimited.test.js +87 -0
  114. package/dist/src/data/transforms/flattenSequence.d.ts +11 -0
  115. package/dist/src/data/transforms/flattenSequence.d.ts.map +1 -0
  116. package/dist/src/data/transforms/flattenSequence.js +35 -0
  117. package/dist/src/data/transforms/flattenSequence.test.js +34 -0
  118. package/dist/src/data/transforms/formula.d.ts +13 -0
  119. package/dist/src/data/transforms/formula.d.ts.map +1 -0
  120. package/dist/src/data/transforms/formula.js +35 -0
  121. package/dist/src/data/transforms/formula.test.js +19 -0
  122. package/dist/src/data/transforms/identifier.d.ts +40 -0
  123. package/dist/src/data/transforms/identifier.d.ts.map +1 -0
  124. package/dist/src/data/transforms/identifier.js +106 -0
  125. package/dist/src/data/transforms/identifier.test.js +83 -0
  126. package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts +10 -0
  127. package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts.map +1 -0
  128. package/dist/src/data/transforms/linearizeGenomicCoordinate.js +97 -0
  129. package/dist/src/data/transforms/measureText.d.ts +18 -0
  130. package/dist/src/data/transforms/measureText.d.ts.map +1 -0
  131. package/dist/src/data/transforms/measureText.js +42 -0
  132. package/dist/src/data/transforms/pileup.d.ts +10 -0
  133. package/dist/src/data/transforms/pileup.d.ts.map +1 -0
  134. package/dist/src/data/transforms/pileup.js +126 -0
  135. package/dist/src/data/transforms/pileup.test.js +70 -0
  136. package/dist/src/data/transforms/project.d.ts +13 -0
  137. package/dist/src/data/transforms/project.d.ts.map +1 -0
  138. package/dist/src/data/transforms/project.js +38 -0
  139. package/dist/src/data/transforms/project.test.js +32 -0
  140. package/dist/src/data/transforms/regexExtract.d.ts +13 -0
  141. package/dist/src/data/transforms/regexExtract.d.ts.map +1 -0
  142. package/dist/src/data/transforms/regexExtract.js +57 -0
  143. package/dist/src/data/transforms/regexExtract.test.js +67 -0
  144. package/dist/src/data/transforms/regexFold.d.ts +14 -0
  145. package/dist/src/data/transforms/regexFold.d.ts.map +1 -0
  146. package/dist/src/data/transforms/regexFold.js +139 -0
  147. package/dist/src/data/transforms/regexFold.test.js +160 -0
  148. package/dist/src/data/transforms/sample.d.ts +42 -0
  149. package/dist/src/data/transforms/sample.d.ts.map +1 -0
  150. package/dist/src/data/transforms/sample.js +99 -0
  151. package/dist/src/data/transforms/sample.test.js +38 -0
  152. package/dist/src/data/transforms/stack.d.ts +11 -0
  153. package/dist/src/data/transforms/stack.d.ts.map +1 -0
  154. package/dist/src/data/transforms/stack.js +134 -0
  155. package/dist/src/data/transforms/stack.test.js +91 -0
  156. package/dist/src/data/transforms/transformFactory.d.ts +12 -0
  157. package/dist/src/data/transforms/transformFactory.d.ts.map +1 -0
  158. package/dist/src/data/transforms/transformFactory.js +59 -0
  159. package/dist/src/encoder/accessor.d.ts +15 -0
  160. package/dist/src/encoder/accessor.d.ts.map +1 -0
  161. package/dist/src/encoder/accessor.js +76 -0
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  163. package/dist/src/encoder/encoder.d.ts +144 -0
  164. package/dist/src/encoder/encoder.d.ts.map +1 -0
  165. package/dist/src/encoder/encoder.js +400 -0
  166. package/dist/src/encoder/encoder.test.js +98 -0
  167. package/dist/src/fonts/Lato-Regular.json +1267 -0
  168. package/dist/src/fonts/Lato-Regular.png +0 -0
  169. package/dist/src/fonts/OFL.txt +93 -0
  170. package/dist/src/fonts/README.md +3 -0
  171. package/dist/src/fonts/bmFontManager.d.ts +182 -0
  172. package/dist/src/fonts/bmFontManager.d.ts.map +1 -0
  173. package/dist/src/fonts/bmFontManager.js +359 -0
  174. package/dist/src/fonts/bmFontMetrics.d.ts +45 -0
  175. package/dist/src/fonts/bmFontMetrics.d.ts.map +1 -0
  176. package/dist/src/fonts/bmFontMetrics.js +108 -0
  177. package/dist/src/genome/genome.d.ts +172 -0
  178. package/dist/src/genome/genome.d.ts.map +1 -0
  179. package/dist/src/genome/genome.js +379 -0
  180. package/dist/src/genome/genome.test.js +226 -0
  181. package/dist/src/genome/genomeStore.d.ts +20 -0
  182. package/dist/src/genome/genomeStore.d.ts.map +1 -0
  183. package/dist/src/genome/genomeStore.js +54 -0
  184. package/dist/src/genome/locusFormat.d.ts +14 -0
  185. package/dist/src/genome/locusFormat.d.ts.map +1 -0
  186. package/dist/src/genome/locusFormat.js +37 -0
  187. package/dist/src/genome/scaleIndex.d.ts +6 -0
  188. package/dist/src/genome/scaleIndex.d.ts.map +1 -0
  189. package/dist/src/genome/scaleIndex.js +165 -0
  190. package/dist/src/genome/scaleIndex.test.js +78 -0
  191. package/dist/src/genome/scaleLocus.d.ts +3 -0
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  194. package/dist/src/genome/scaleLocus.test.js +4 -0
  195. package/dist/src/genomeSpy.d.ts +141 -0
  196. package/dist/src/genomeSpy.d.ts.map +1 -0
  197. package/dist/src/genomeSpy.js +788 -0
  198. package/dist/src/gl/arrayBuilder.d.ts +71 -0
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  203. package/dist/src/gl/dataToVertices.js +639 -0
  204. package/dist/src/gl/includes/common.glsl.js +2 -0
  205. package/dist/src/gl/includes/picking.fragment.glsl.js +2 -0
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  222. package/dist/src/img/bowtie.svg +1 -0
  223. package/dist/src/img/genomespy-favicon.svg +34 -0
  224. package/dist/src/index.d.ts +15 -0
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@@ -0,0 +1,38 @@
1
+ import { expect, test } from "vitest";
2
+ import SampleTransform from "./sample";
3
+ import { extent } from "d3-array";
4
+ import { createChain } from "../../view/flowBuilder";
5
+
6
+ test("SampleTransform produces roughly uniform distributions", () => {
7
+ const size = 10;
8
+ const n = 20;
9
+ const rounds = 10000;
10
+
11
+ const freqs = [];
12
+ for (let i = 0; i < n; i++) {
13
+ freqs[i] = 0;
14
+ }
15
+
16
+ const { dataSource, collector } = createChain(
17
+ new SampleTransform({ type: "sample", size })
18
+ );
19
+
20
+ for (let r = 0; r < rounds; r++) {
21
+ for (let i = 0; i < n; i++) {
22
+ dataSource.handle({ data: i });
23
+ }
24
+ dataSource.complete();
25
+
26
+ for (const datum of collector.getData()) {
27
+ freqs[datum.data] = freqs[datum.data] + 1;
28
+ }
29
+
30
+ dataSource.reset();
31
+ }
32
+
33
+ const e = extent(freqs);
34
+
35
+ // Not a deterministic test! TODO: Come up with some sensical testing method
36
+ expect(e[0]).toBeGreaterThan(4800);
37
+ expect(e[1]).toBeLessThan(5200);
38
+ });
@@ -0,0 +1,11 @@
1
+ export default class StackTransform extends FlowNode {
2
+ /**
3
+ * @param {import("../../spec/transform").StackParams} params
4
+ */
5
+ constructor(params: import("../../spec/transform").StackParams);
6
+ params: import("../../spec/transform").StackParams;
7
+ /** @type {any[]} */
8
+ buffer: any[];
9
+ }
10
+ import FlowNode from "../flowNode";
11
+ //# sourceMappingURL=stack.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"stack.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/stack.js"],"names":[],"mappings":"AAKA;IAKI;;OAEG;IACH,oBAFW,OAAO,sBAAsB,EAAE,WAAW,EAQpD;IAJG,mDAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;CAmHvB;qBAnI2C,aAAa"}
@@ -0,0 +1,134 @@
1
+ import { compare } from "vega-util";
2
+ import { groups as d3groups, sum as d3sum } from "d3-array";
3
+ import FlowNode, { BEHAVIOR_MODIFIES } from "../flowNode";
4
+ import { field } from "../../utils/field";
5
+
6
+ export default class StackTransform extends FlowNode {
7
+ get behavior() {
8
+ return BEHAVIOR_MODIFIES;
9
+ }
10
+
11
+ /**
12
+ * @param {import("../../spec/transform").StackParams} params
13
+ */
14
+ constructor(params) {
15
+ super();
16
+ this.params = params;
17
+
18
+ /** @type {any[]} */
19
+ this.buffer = [];
20
+ }
21
+
22
+ reset() {
23
+ this.buffer = [];
24
+ }
25
+
26
+ /**
27
+ *
28
+ * @param {import("../flowNode").Datum} datum
29
+ */
30
+ handle(datum) {
31
+ this.buffer.push(datum);
32
+ }
33
+
34
+ complete() {
35
+ const params = this.params;
36
+
37
+ const as = params.as || ["y0", "y1"]; // TODO: Validate
38
+
39
+ const comparator = params.sort
40
+ ? compare(params.sort.field, params.sort.order)
41
+ : undefined;
42
+
43
+ const valueAccessor = params.field ? field(params.field) : () => 1;
44
+
45
+ const groupFields = params.groupby.map((f) => field(f));
46
+
47
+ const groups = d3groups(this.buffer, (row) =>
48
+ groupFields.map((f) => f(row)).join()
49
+ ).map((a) => a[1]);
50
+
51
+ /** @type {(datum: any) => boolean} */
52
+ let inclusionPredicate = (_datum) => true;
53
+
54
+ if (params.baseField) {
55
+ const baseAccessor = field(params.baseField);
56
+ inclusionPredicate = (datum) => baseAccessor(datum) !== null;
57
+ }
58
+
59
+ /** @type {(value: number, sum: number) => number} */
60
+ let offsetF;
61
+
62
+ /** @type {(values: number[], accessor: (datum: any) => number) => number} */
63
+ let sumF;
64
+
65
+ switch (params.offset) {
66
+ case "normalize":
67
+ offsetF = (value, sum) => value / sum;
68
+ sumF = (values, accessor) => d3sum(values, accessor);
69
+ break;
70
+ case "center":
71
+ offsetF = (value, sum) => value - sum / 2;
72
+ sumF = (values, accessor) => d3sum(values, accessor);
73
+ break;
74
+ case "information":
75
+ {
76
+ // Sequence logos: a new way to display consensus sequences (Schneider and Stephens)
77
+ // doi://10.1093/nar/18.20.6097
78
+
79
+ const maxBits = Math.log2(params.cardinality ?? 4);
80
+ offsetF = (value, sum) => value / sum;
81
+ sumF = (values, accessor) => {
82
+ const e = 0; // TODO: Correction factor for small sample sizes
83
+
84
+ const gaps = d3sum(
85
+ values,
86
+ (d) => +!inclusionPredicate(d)
87
+ );
88
+ const total = d3sum(values, accessor);
89
+ const nonGaps = total - gaps;
90
+
91
+ let H = 0;
92
+ for (let i = 0; i < values.length; i++) {
93
+ const datum = values[i];
94
+ if (inclusionPredicate(datum)) {
95
+ const b = accessor(datum) / nonGaps;
96
+ H -= b * Math.log2(b);
97
+ }
98
+ }
99
+
100
+ return (
101
+ (nonGaps / (maxBits - (H + e))) * (nonGaps / total)
102
+ );
103
+ };
104
+ }
105
+ break;
106
+ default:
107
+ offsetF = (value, sum) => value;
108
+ sumF = (_values, _accessor) => 1;
109
+ }
110
+
111
+ for (const group of groups) {
112
+ if (comparator) {
113
+ group.sort(comparator);
114
+ }
115
+
116
+ const sum = sumF(group, valueAccessor);
117
+
118
+ let prev = 0;
119
+ for (const datum of group) {
120
+ const current = prev + valueAccessor(datum);
121
+
122
+ if (inclusionPredicate(datum)) {
123
+ datum[as[0]] = offsetF(prev, sum);
124
+ datum[as[1]] = offsetF(current, sum);
125
+
126
+ this._propagate(datum);
127
+ prev = current;
128
+ }
129
+ }
130
+ }
131
+
132
+ super.complete();
133
+ }
134
+ }
@@ -0,0 +1,91 @@
1
+ import { describe, expect, test } from "vitest";
2
+ import { processData } from "../flowTestUtils";
3
+ import StackTransform from "./stack";
4
+
5
+ const sampleData = [
6
+ { group: "a", choice: "q", value: 1 },
7
+ { group: "b", choice: "x", value: 1 },
8
+ { group: "b", choice: "y", value: 3 },
9
+ ];
10
+
11
+ /** @type {import("./stack").StackParams} */
12
+ const baseConf = {
13
+ type: "stack",
14
+ field: "value",
15
+ groupby: ["group"],
16
+ sort: {
17
+ field: "value",
18
+ order: "ascending",
19
+ },
20
+ offset: "zero",
21
+ as: ["z0", "z1"],
22
+ };
23
+
24
+ /**
25
+ *
26
+ * @param {import("./stack").StackParams} params
27
+ * @param {any[]} data
28
+ */
29
+ function transform(params, data) {
30
+ return processData(new StackTransform(params), data);
31
+ }
32
+
33
+ describe("Stack transform", () => {
34
+ test("No field", () => {
35
+ const conf = Object.assign({}, baseConf, {
36
+ field: undefined,
37
+ });
38
+
39
+ expect(transform(conf, sampleData)).toEqual([
40
+ { group: "a", choice: "q", value: 1, z0: 0, z1: 1 },
41
+ { group: "b", choice: "x", value: 1, z0: 0, z1: 1 },
42
+ { group: "b", choice: "y", value: 3, z0: 1, z1: 2 },
43
+ ]);
44
+ });
45
+
46
+ test("Zero offset", () => {
47
+ expect(transform(baseConf, sampleData)).toEqual([
48
+ { group: "a", choice: "q", value: 1, z0: 0, z1: 1 },
49
+ { group: "b", choice: "x", value: 1, z0: 0, z1: 1 },
50
+ { group: "b", choice: "y", value: 3, z0: 1, z1: 4 },
51
+ ]);
52
+ });
53
+
54
+ test("Normalize offset", () => {
55
+ const conf = Object.assign({}, baseConf, {
56
+ offset: "normalize",
57
+ });
58
+
59
+ expect(transform(conf, sampleData)).toEqual([
60
+ { group: "a", choice: "q", value: 1, z0: 0, z1: 1 },
61
+ { group: "b", choice: "x", value: 1, z0: 0, z1: 0.25 },
62
+ { group: "b", choice: "y", value: 3, z0: 0.25, z1: 1 },
63
+ ]);
64
+ });
65
+
66
+ test("Center offset", () => {
67
+ const conf = Object.assign({}, baseConf, {
68
+ offset: "center",
69
+ });
70
+
71
+ expect(transform(conf, sampleData)).toEqual([
72
+ { group: "a", choice: "q", value: 1, z0: -0.5, z1: 0.5 },
73
+ { group: "b", choice: "x", value: 1, z0: -2, z1: -1 },
74
+ { group: "b", choice: "y", value: 3, z0: -1, z1: 2 },
75
+ ]);
76
+ });
77
+
78
+ test("Descending sort", () => {
79
+ const conf = Object.assign({}, baseConf, {
80
+ sort: {
81
+ field: "value",
82
+ order: "descending",
83
+ },
84
+ });
85
+ expect(transform(conf, sampleData)).toEqual([
86
+ { group: "a", choice: "q", value: 1, z0: 0, z1: 1 },
87
+ { group: "b", choice: "y", value: 3, z0: 0, z1: 3 },
88
+ { group: "b", choice: "x", value: 1, z0: 3, z1: 4 },
89
+ ]);
90
+ });
91
+ });
@@ -0,0 +1,12 @@
1
+ /**
2
+ * @param {import("../../spec/transform").TransformParamsBase} params
3
+ * @param {import("../../view/view").default} [view]
4
+ */
5
+ export default function createTransform(params: import("../../spec/transform").TransformParamsBase, view?: import("../../view/view").default): import("../flowNode").default;
6
+ /**
7
+ * TODO: Make this dynamic
8
+ *
9
+ * @type {Record<string, new (params: any, view?: import("../../view/view").default) => import("../flowNode").default>}
10
+ */
11
+ export const transforms: Record<string, new (params: any, view?: import("../../view/view").default) => import("../flowNode").default>;
12
+ //# sourceMappingURL=transformFactory.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"transformFactory.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/transformFactory.js"],"names":[],"mappings":"AA+CA;;;GAGG;AACH,gDAHW,OAAO,sBAAsB,EAAE,mBAAmB,SAClD,OAAO,iBAAiB,EAAE,OAAO,iCAS3C;AAtCD;;;;GAIG;AACH,qDAFsC,GAAG,SAAS,OAAO,iBAAiB,EAAE,OAAO,KAAK,OAAO,aAAa,EAAE,OAAO,EAsBnH"}
@@ -0,0 +1,59 @@
1
+ import Collector from "../collector";
2
+ import CoverageTransform from "./coverage";
3
+ import FilterScoredLabelsTransform from "./filterScoredLabels";
4
+ import FilterTransform from "./filter";
5
+ import FlattenTransform from "./flatten";
6
+ import FlattenCompressedExonsTransform from "./flattenCompressedExons";
7
+ import FlattenDelimitedTransform from "./flattenDelimited";
8
+ import FormulaTransform from "./formula";
9
+ import LinearizeGenomicCoordinate from "./linearizeGenomicCoordinate";
10
+ import MeasureTextTransform from "./measureText";
11
+ import PileupTransform from "./pileup";
12
+ import ProjectTransform from "./project";
13
+ import RegexExtractTransform from "./regexExtract";
14
+ import RegexFoldTransform from "./regexFold";
15
+ import SampleTransform from "./sample";
16
+ import StackTransform from "./stack";
17
+ import FlattenSequenceTransform from "./flattenSequence";
18
+ import AggregateTransform from "./aggregate";
19
+ import IdentifierTransform from "./identifier";
20
+
21
+ /**
22
+ * TODO: Make this dynamic
23
+ *
24
+ * @type {Record<string, new (params: any, view?: import("../../view/view").default) => import("../flowNode").default>}
25
+ */
26
+ export const transforms = {
27
+ aggregate: AggregateTransform,
28
+ collect: Collector,
29
+ coverage: CoverageTransform,
30
+ filterScoredLabels: FilterScoredLabelsTransform,
31
+ filter: FilterTransform,
32
+ flatten: FlattenTransform,
33
+ flattenCompressedExons: FlattenCompressedExonsTransform,
34
+ flattenDelimited: FlattenDelimitedTransform,
35
+ flattenSequence: FlattenSequenceTransform,
36
+ formula: FormulaTransform,
37
+ identifier: IdentifierTransform,
38
+ linearizeGenomicCoordinate: LinearizeGenomicCoordinate,
39
+ measureText: MeasureTextTransform,
40
+ pileup: PileupTransform,
41
+ project: ProjectTransform,
42
+ regexExtract: RegexExtractTransform,
43
+ regexFold: RegexFoldTransform,
44
+ sample: SampleTransform,
45
+ stack: StackTransform,
46
+ };
47
+
48
+ /**
49
+ * @param {import("../../spec/transform").TransformParamsBase} params
50
+ * @param {import("../../view/view").default} [view]
51
+ */
52
+ export default function createTransform(params, view) {
53
+ const Transform = transforms[params.type];
54
+ if (Transform) {
55
+ return new Transform(params, view);
56
+ } else {
57
+ throw new Error("Unknown transform: " + params.type);
58
+ }
59
+ }
@@ -0,0 +1,15 @@
1
+ export default class AccessorFactory {
2
+ /** @type {(function(import("../spec/channel").ChannelDef):Accessor)[]} */
3
+ accessorCreators: ((arg0: import("../spec/channel").ChannelDef) => import("../types/encoder").Accessor)[];
4
+ /**
5
+ *
6
+ * @param {function(import("../spec/channel").ChannelDef):Accessor} creator
7
+ */
8
+ register(creator: (arg0: import("../spec/channel").ChannelDef) => import("../types/encoder").Accessor): void;
9
+ /**
10
+ *
11
+ * @param {import("../spec/channel").ChannelDef} encoding
12
+ */
13
+ createAccessor(encoding: import("../spec/channel").ChannelDef): import("../types/encoder").Accessor;
14
+ }
15
+ //# sourceMappingURL=accessor.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"accessor.d.ts","sourceRoot":"","sources":["../../../src/encoder/accessor.js"],"names":[],"mappings":"AAMA;IAKQ,0EAA0E;IAC1E,0BADqB,OAAO,iBAAiB,EAAE,UAAU,4CAC/B;IAkC9B;;;OAGG;IACH,yBAFoB,OAAO,iBAAiB,EAAE,UAAU,gDAIvD;IAED;;;OAGG;IACH,yBAFW,OAAO,iBAAiB,EAAE,UAAU,uCAS9C;CACJ"}
@@ -0,0 +1,76 @@
1
+ import createFunction from "../utils/expression";
2
+
3
+ import { accessorFields, constant } from "vega-util";
4
+ import { isDatumDef, isExprDef, isFieldDef } from "./encoder";
5
+ import { field } from "../utils/field";
6
+
7
+ export default class AccessorFactory {
8
+ /**
9
+ * @typedef {import("../types/encoder").Accessor} Accessor
10
+ */
11
+ constructor() {
12
+ /** @type {(function(import("../spec/channel").ChannelDef):Accessor)[]} */
13
+ this.accessorCreators = [];
14
+
15
+ this.register((channelDef) => {
16
+ if (isFieldDef(channelDef)) {
17
+ try {
18
+ const accessor = /** @type {Accessor} */ (
19
+ field(channelDef.field)
20
+ );
21
+ accessor.constant = false;
22
+ accessor.fields = accessorFields(accessor);
23
+ return accessor;
24
+ } catch (e) {
25
+ throw new Error(`Invalid field definition: ${e.message}`);
26
+ }
27
+ }
28
+ });
29
+
30
+ this.register((channelDef) =>
31
+ isExprDef(channelDef)
32
+ ? createExpressionAccessor(channelDef.expr)
33
+ : undefined
34
+ );
35
+
36
+ this.register((channelDef) => {
37
+ if (isDatumDef(channelDef)) {
38
+ const c = /** @type {any} */ (constant(channelDef.datum));
39
+ const accessor = /** @type {Accessor} */ (c);
40
+ accessor.constant = true; // Can be optimized downstream
41
+ accessor.fields = [];
42
+ return accessor;
43
+ }
44
+ });
45
+ }
46
+
47
+ /**
48
+ *
49
+ * @param {function(import("../spec/channel").ChannelDef):Accessor} creator
50
+ */
51
+ register(creator) {
52
+ this.accessorCreators.push(creator);
53
+ }
54
+
55
+ /**
56
+ *
57
+ * @param {import("../spec/channel").ChannelDef} encoding
58
+ */
59
+ createAccessor(encoding) {
60
+ for (const creator of this.accessorCreators) {
61
+ const accessor = creator(encoding);
62
+ if (accessor) {
63
+ return accessor;
64
+ }
65
+ }
66
+ }
67
+ }
68
+
69
+ /**
70
+ * @param {string} expr
71
+ */
72
+ function createExpressionAccessor(expr) {
73
+ const accessor = /** @type {Accessor} */ (createFunction(expr));
74
+ accessor.constant = accessor.fields.length == 0; // Not bulletproof, eh
75
+ return accessor;
76
+ }
@@ -0,0 +1,47 @@
1
+ import { expect, test } from "vitest";
2
+ import AccessorFactory from "./accessor";
3
+
4
+ const af = new AccessorFactory();
5
+
6
+ const datum = {
7
+ a: 1,
8
+ b: 2,
9
+ "x.c": 3,
10
+ };
11
+
12
+ test("Creates a field accessor", () => {
13
+ const a = af.createAccessor({ field: "a" });
14
+ expect(a(datum)).toEqual(1);
15
+ expect(a.constant).toBeFalsy();
16
+ expect(a.fields).toEqual(["a"]);
17
+ });
18
+
19
+ test("Creates an expression accessor", () => {
20
+ const a = af.createAccessor({ expr: `datum.b + datum['x\.c']` });
21
+ expect(a(datum)).toEqual(5);
22
+ expect(a.constant).toBeFalsy();
23
+ expect(a.fields.sort()).toEqual(["b", "x.c"].sort());
24
+ });
25
+
26
+ test("Creates a constant accessor", () => {
27
+ const a = af.createAccessor({ datum: 0 });
28
+ expect(a(datum)).toEqual(0);
29
+ expect(a.constant).toBeTruthy();
30
+ expect(a.fields).toEqual([]);
31
+ });
32
+
33
+ test("Returns undefined on incomplete encoding spec", () => {
34
+ expect(af.createAccessor({})).toBeUndefined();
35
+ });
36
+
37
+ test("Registers and creates a custom accessor", () => {
38
+ const af = new AccessorFactory();
39
+ af.register((encoding) => {
40
+ if (encoding.iddqd && encoding.idkfa) {
41
+ return (datum) =>
42
+ `${datum[encoding.iddqd]}-${datum[encoding.idkfa]}`;
43
+ }
44
+ });
45
+
46
+ expect(af.createAccessor({ iddqd: "a", idkfa: "b" })(datum)).toEqual("1-2");
47
+ });
@@ -0,0 +1,144 @@
1
+ /**
2
+ * Creates an object that contains encoders for every channel of a mark
3
+ *
4
+ * TODO: This should actually receive the mark as parameter
5
+ *
6
+ * TODO: This method should have a test. But how to mock Mark...
7
+ *
8
+ * @param {import("../marks/mark").default} mark
9
+ * @param {import("../spec/channel").Encoding} [encoding] Taken from the mark if not provided
10
+ * @returns {Partial<Record<Channel, Encoder>>}
11
+ */
12
+ export default function createEncoders(mark: import("../marks/mark").default, encoding?: import("../spec/channel").Encoding): Partial<Record<import("../spec/channel").Channel, import("../types/encoder").Encoder>>;
13
+ /**
14
+ *
15
+ * @param {import("../spec/channel").ChannelDef} channelDef
16
+ * @param {any} scale
17
+ * @param {Accessor} accessor
18
+ * @param {Channel} channel
19
+ * @returns {Encoder}
20
+ */
21
+ export function createEncoder(channelDef: import("../spec/channel").ChannelDef, scale: any, accessor: import("../types/encoder").Accessor, channel: import("../spec/channel").Channel): import("../types/encoder").Encoder;
22
+ /**
23
+ * TODO: Move to a more generic place
24
+ *
25
+ * @param {import("../spec/channel").ChannelDef} channelDef
26
+ * @returns {channelDef is import("../spec/channel").ValueDef}
27
+ */
28
+ export function isValueDef(channelDef: import("../spec/channel").ChannelDef): channelDef is import("../spec/channel").ValueDef<import("../spec/channel").Scalar>;
29
+ /**
30
+ * @param {import("../spec/channel").ChannelDef} channelDef
31
+ * @returns {channelDef is import("../spec/channel").FieldDefBase<string>}
32
+ */
33
+ export function isFieldDef(channelDef: import("../spec/channel").ChannelDef): channelDef is import("../spec/channel").FieldDefBase<string>;
34
+ /**
35
+ * @param {import("../spec/channel").ChannelDef} channelDef
36
+ * @returns {channelDef is import("../spec/channel").DatumDef}
37
+ */
38
+ export function isDatumDef(channelDef: import("../spec/channel").ChannelDef): channelDef is import("../spec/channel").DatumDef;
39
+ /**
40
+ * @param {import("../spec/channel").ChannelDef} channelDef
41
+ * @returns {channelDef is import("../spec/channel").ChannelDefWithScale}
42
+ */
43
+ export function isChannelDefWithScale(channelDef: import("../spec/channel").ChannelDef): channelDef is import("../spec/channel").ChannelDefWithScale;
44
+ /**
45
+ * @param {import("../view/unitView").default} view
46
+ * @param {import("../spec/channel").Channel} channel
47
+ */
48
+ export function getChannelDefWithScale(view: import("../view/unitView").default, channel: import("../spec/channel").Channel): import("../spec/channel").ChromPosDef | import("../spec/channel").PositionDatumDef | import("../spec/channel").MarkPropExprDef<import("../spec/channel").Type> | import("../spec/channel").MarkPropDatumDef<import("../spec/channel").Type> | import("../spec/channel").MarkPropDatumDef<import("../spec/channel").TypeForShape> | import("../spec/channel").PositionFieldDef<string> | import("../spec/channel").MarkPropFieldDef<string, import("../spec/channel").Type> | import("../spec/channel").MarkPropFieldDef<string, import("../spec/channel").TypeForShape>;
49
+ /**
50
+ * @param {import("../spec/channel").ChannelDef} channelDef
51
+ * @returns {channelDef is import("../spec/channel").ChromPosDef}
52
+ */
53
+ export function isChromPosDef(channelDef: import("../spec/channel").ChannelDef): channelDef is import("../spec/channel").ChromPosDef;
54
+ /**
55
+ * @param {import("../spec/channel").ChannelDef} channelDef
56
+ * @returns {channelDef is import("../spec/channel").ExprDef}
57
+ */
58
+ export function isExprDef(channelDef: import("../spec/channel").ChannelDef): channelDef is import("../spec/channel").ExprDef;
59
+ /**
60
+ * @param {import("../spec/channel").Channel} channel
61
+ * @returns {channel is import("../spec/channel").PrimaryPositionalChannel}
62
+ */
63
+ export function isPrimaryPositionalChannel(channel: import("../spec/channel").Channel): channel is import("../spec/channel").PrimaryPositionalChannel;
64
+ /**
65
+ * @param {import("../spec/channel").Channel} channel
66
+ * @returns {channel is import("../spec/channel").PositionalChannel}
67
+ */
68
+ export function isPositionalChannel(channel: import("../spec/channel").Channel): channel is import("../spec/channel").PositionalChannel;
69
+ /**
70
+ *
71
+ * @param {string} channel
72
+ */
73
+ export function isSecondaryChannel(channel: string): boolean;
74
+ /**
75
+ * Return the matching secondary channel or throws if one does not exist.
76
+ *
77
+ * @param {import("../spec/channel").Channel} primaryChannel
78
+ */
79
+ export function getSecondaryChannel(primaryChannel: import("../spec/channel").Channel): import("../spec/channel").SecondaryPositionalChannel;
80
+ /**
81
+ * Finds the primary channel for the provided channel, which may be
82
+ * the primary or secondary.
83
+ *
84
+ * @param {import("../spec/channel").Channel} channel
85
+ */
86
+ export function getPrimaryChannel(channel: import("../spec/channel").Channel): import("../spec/channel").Channel;
87
+ /**
88
+ * Returns an array that contains the given channel and its secondary channel if one exists.
89
+ *
90
+ * @param {import("../spec/channel").Channel} channel
91
+ */
92
+ export function getChannelWithSecondarys(channel: import("../spec/channel").Channel): import("../spec/channel").Channel[];
93
+ /**
94
+ * @param {import("../spec/channel").Channel} channel
95
+ */
96
+ export function isColorChannel(channel: import("../spec/channel").Channel): boolean;
97
+ /**
98
+ * Returns true if the channel has a discrete range.
99
+ *
100
+ * @param {import("../spec/channel").Channel} channel
101
+ */
102
+ export function isDiscreteChannel(channel: import("../spec/channel").Channel): boolean;
103
+ /**
104
+ * @param {import("../spec/channel").Channel} channel
105
+ * @returns {channel is import("../spec/channel").ChannelWithScale}
106
+ */
107
+ export function isChannelWithScale(channel: import("../spec/channel").Channel): channel is import("../spec/channel").ChannelWithScale;
108
+ /**
109
+ * Returns valid discrete values for a discrete channel.
110
+ *
111
+ * @param {import("../spec/channel").Channel} channel
112
+ * @returns {any[]}
113
+ */
114
+ export function getDiscreteRange(channel: import("../spec/channel").Channel): any[];
115
+ /**
116
+ * @param {import("../spec/channel").Channel} channel
117
+ * @returns {function(any):number}
118
+ */
119
+ export function getDiscreteRangeMapper(channel: import("../spec/channel").Channel): (arg0: any) => number;
120
+ /**
121
+ * @type {import("../spec/channel").PrimaryPositionalChannel[]}
122
+ */
123
+ export const primaryPositionalChannels: import("../spec/channel").PrimaryPositionalChannel[];
124
+ /**
125
+ * @type {import("../spec/channel").SecondaryPositionalChannel[]}
126
+ */
127
+ export const secondaryPositionalChannels: import("../spec/channel").SecondaryPositionalChannel[];
128
+ /**
129
+ * @type {import("../spec/channel").PositionalChannel[]}
130
+ */
131
+ export const positionalChannels: import("../spec/channel").PositionalChannel[];
132
+ /**
133
+ * Map primary channels to secondarys
134
+ *
135
+ * @type {Partial<Record<import("../spec/channel").Channel, import("../spec/channel").SecondaryPositionalChannel>>}
136
+ */
137
+ export const secondaryChannels: Partial<Record<import("../spec/channel").Channel, import("../spec/channel").SecondaryPositionalChannel>>;
138
+ /**
139
+ * Map secondary channels to primaries
140
+ *
141
+ * @type {Partial<Record<import("../spec/channel").Channel, import("../spec/channel").Channel>>}
142
+ */
143
+ export const primaryChannels: Partial<Record<import("../spec/channel").Channel, import("../spec/channel").Channel>>;
144
+ //# sourceMappingURL=encoder.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"encoder.d.ts","sourceRoot":"","sources":["../../../src/encoder/encoder.js"],"names":[],"mappings":"AAIA;;;;;;;;;;GAUG;AACH,6CAJW,OAAO,eAAe,EAAE,OAAO,aAC/B,OAAO,iBAAiB,EAAE,QAAQ,0FAsC5C;AAED;;;;;;;GAOG;AACH,0CANW,OAAO,iBAAiB,EAAE,UAAU,SACpC,GAAG,iIAyFb;AAED;;;;;GAKG;AACH,uCAHW,OAAO,iBAAiB,EAAE,UAAU,sFAK9C;AAED;;;GAGG;AACH,uCAHW,OAAO,iBAAiB,EAAE,UAAU,gEAK9C;AAED;;;GAGG;AACH,uCAHW,OAAO,iBAAiB,EAAE,UAAU,oDAK9C;AAED;;;GAGG;AACH,kDAHW,OAAO,iBAAiB,EAAE,UAAU,+DAW9C;AAED;;;GAGG;AACH,6CAHW,OAAO,kBAAkB,EAAE,OAAO,WAClC,OAAO,iBAAiB,EAAE,OAAO,2iBAS3C;AAED;;;GAGG;AACH,0CAHW,OAAO,iBAAiB,EAAE,UAAU,uDAK9C;AAED;;;GAGG;AACH,sCAHW,OAAO,iBAAiB,EAAE,UAAU,mDAK9C;AAoBD;;;GAGG;AACH,oDAHW,OAAO,iBAAiB,EAAE,OAAO,iEAM3C;AAED;;;GAGG;AACH,6CAHW,OAAO,iBAAiB,EAAE,OAAO,0DAM3C;AAqBD;;;GAGG;AACH,4CAFW,MAAM,WAIhB;AAED;;;;GAIG;AACH,oDAFW,OAAO,iBAAiB,EAAE,OAAO,wDAS3C;AAED;;;;;GAKG;AACH,2CAFW,OAAO,iBAAiB,EAAE,OAAO,qCAI3C;AAED;;;;GAIG;AACH,kDAFW,OAAO,iBAAiB,EAAE,OAAO,uCAM3C;AAED;;GAEG;AACH,wCAFW,OAAO,iBAAiB,EAAE,OAAO,WAI3C;AAED;;;;GAIG;AACH,2CAFW,OAAO,iBAAiB,EAAE,OAAO,WAI3C;AAED;;;GAGG;AACH,4CAHW,OAAO,iBAAiB,EAAE,OAAO,yDAuB3C;AAED;;;;;GAKG;AACH,0CAHW,OAAO,iBAAiB,EAAE,OAAO,GAC/B,GAAG,EAAE,CAkBjB;AAED;;;GAGG;AACH,gDAHW,OAAO,iBAAiB,EAAE,OAAO,UACtB,GAAG,KAAE,MAAM,CAkBhC;AAxLD;;GAEG;AACH,wCAFU,OAAO,iBAAiB,EAAE,wBAAwB,EAAE,CAEV;AAEpD;;GAEG;AACH,0CAFU,OAAO,iBAAiB,EAAE,0BAA0B,EAAE,CAER;AAExD;;GAEG;AACH,iCAFU,OAAO,iBAAiB,EAAE,iBAAiB,EAAE,CAKrD;AAoBF;;;;GAIG;AACH,gCAFU,QAAQ,OAAO,OAAO,iBAAiB,EAAE,OAAO,EAAE,OAAO,iBAAiB,EAAE,0BAA0B,CAAC,CAAC,CAKhH;AAEF;;;;GAIG;AACH,8BAFU,QAAQ,OAAO,OAAO,iBAAiB,EAAE,OAAO,EAAE,OAAO,iBAAiB,EAAE,OAAO,CAAC,CAAC,CAI7F"}