@genome-spy/core 0.30.0 → 0.30.3

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 (234) hide show
  1. package/dist/index.es.js +16379 -0
  2. package/dist/index.js +43 -43
  3. package/package.json +10 -7
  4. package/src/data/collector.js +0 -183
  5. package/src/data/collector.test.js +0 -84
  6. package/src/data/dataFlow.js +0 -148
  7. package/src/data/dataFlow.test.js +0 -5
  8. package/src/data/facetNode.js +0 -17
  9. package/src/data/flow.test.js +0 -72
  10. package/src/data/flowBatch.d.ts +0 -40
  11. package/src/data/flowNode.js +0 -283
  12. package/src/data/flowNode.test.js +0 -50
  13. package/src/data/flowOptimizer.js +0 -123
  14. package/src/data/flowOptimizer.test.js +0 -193
  15. package/src/data/flowTestUtils.js +0 -63
  16. package/src/data/formats/fasta.js +0 -32
  17. package/src/data/formats/fasta.test.js +0 -27
  18. package/src/data/sources/dataSource.js +0 -22
  19. package/src/data/sources/dataSourceFactory.js +0 -24
  20. package/src/data/sources/dataUtils.js +0 -78
  21. package/src/data/sources/dynamicCallbackSource.js +0 -57
  22. package/src/data/sources/dynamicSource.js +0 -37
  23. package/src/data/sources/inlineSource.js +0 -67
  24. package/src/data/sources/inlineSource.test.js +0 -56
  25. package/src/data/sources/namedSource.js +0 -79
  26. package/src/data/sources/sequenceSource.js +0 -46
  27. package/src/data/sources/sequenceSource.test.js +0 -46
  28. package/src/data/sources/urlSource.js +0 -74
  29. package/src/data/transforms/aggregate.js +0 -70
  30. package/src/data/transforms/clone.js +0 -40
  31. package/src/data/transforms/clone.test.js +0 -11
  32. package/src/data/transforms/coverage.js +0 -187
  33. package/src/data/transforms/coverage.test.js +0 -123
  34. package/src/data/transforms/filter.js +0 -37
  35. package/src/data/transforms/filter.test.js +0 -18
  36. package/src/data/transforms/filterScoredLabels.js +0 -134
  37. package/src/data/transforms/flattenCompressedExons.js +0 -57
  38. package/src/data/transforms/flattenDelimited.js +0 -74
  39. package/src/data/transforms/flattenDelimited.test.js +0 -87
  40. package/src/data/transforms/flattenSequence.js +0 -39
  41. package/src/data/transforms/flattenSequence.test.js +0 -34
  42. package/src/data/transforms/formula.js +0 -39
  43. package/src/data/transforms/formula.test.js +0 -19
  44. package/src/data/transforms/identifier.js +0 -108
  45. package/src/data/transforms/identifier.test.js +0 -83
  46. package/src/data/transforms/linearizeGenomicCoordinate.js +0 -101
  47. package/src/data/transforms/measureText.js +0 -44
  48. package/src/data/transforms/pileup.js +0 -128
  49. package/src/data/transforms/pileup.test.js +0 -70
  50. package/src/data/transforms/project.js +0 -41
  51. package/src/data/transforms/project.test.js +0 -32
  52. package/src/data/transforms/regexExtract.js +0 -61
  53. package/src/data/transforms/regexExtract.test.js +0 -67
  54. package/src/data/transforms/regexFold.js +0 -141
  55. package/src/data/transforms/regexFold.test.js +0 -160
  56. package/src/data/transforms/sample.js +0 -101
  57. package/src/data/transforms/sample.test.js +0 -38
  58. package/src/data/transforms/stack.js +0 -137
  59. package/src/data/transforms/stack.test.js +0 -91
  60. package/src/data/transforms/transformFactory.js +0 -60
  61. package/src/embedApi.d.ts +0 -67
  62. package/src/encoder/accessor.js +0 -82
  63. package/src/encoder/accessor.test.js +0 -47
  64. package/src/encoder/encoder.js +0 -394
  65. package/src/encoder/encoder.test.js +0 -98
  66. package/src/fonts/Lato-Regular.json +0 -1267
  67. package/src/fonts/Lato-Regular.png +0 -0
  68. package/src/fonts/OFL.txt +0 -93
  69. package/src/fonts/README.md +0 -3
  70. package/src/fonts/bmFont.d.ts +0 -58
  71. package/src/fonts/bmFontManager.js +0 -357
  72. package/src/fonts/bmFontMetrics.js +0 -108
  73. package/src/genome/genome.js +0 -317
  74. package/src/genome/genome.test.js +0 -188
  75. package/src/genome/genomeStore.js +0 -54
  76. package/src/genome/locusFormat.js +0 -31
  77. package/src/genome/scaleIndex.d.ts +0 -38
  78. package/src/genome/scaleIndex.js +0 -166
  79. package/src/genome/scaleIndex.test.js +0 -78
  80. package/src/genome/scaleLocus.d.ts +0 -11
  81. package/src/genome/scaleLocus.js +0 -108
  82. package/src/genome/scaleLocus.test.js +0 -4
  83. package/src/genomeSpy.js +0 -785
  84. package/src/gl/arrayBuilder.js +0 -199
  85. package/src/gl/dataToVertices.js +0 -636
  86. package/src/gl/includes/common.glsl +0 -63
  87. package/src/gl/includes/picking.fragment.glsl +0 -1
  88. package/src/gl/includes/picking.vertex.glsl +0 -27
  89. package/src/gl/includes/sampleFacet.glsl +0 -107
  90. package/src/gl/includes/scales.glsl +0 -112
  91. package/src/gl/link.fragment.glsl +0 -18
  92. package/src/gl/link.vertex.glsl +0 -111
  93. package/src/gl/point.fragment.glsl +0 -123
  94. package/src/gl/point.vertex.glsl +0 -129
  95. package/src/gl/rect.fragment.glsl +0 -51
  96. package/src/gl/rect.vertex.glsl +0 -114
  97. package/src/gl/rule.fragment.glsl +0 -52
  98. package/src/gl/rule.vertex.glsl +0 -89
  99. package/src/gl/text.fragment.glsl +0 -31
  100. package/src/gl/text.vertex.glsl +0 -246
  101. package/src/gl/webGLHelper.js +0 -504
  102. package/src/img/bowtie.svg +0 -1
  103. package/src/img/genomespy-favicon.svg +0 -34
  104. package/src/index.html +0 -11
  105. package/src/index.js +0 -128
  106. package/src/marks/link.js +0 -175
  107. package/src/marks/mark.js +0 -975
  108. package/src/marks/markUtils.js +0 -125
  109. package/src/marks/pointMark.js +0 -251
  110. package/src/marks/rectMark.js +0 -241
  111. package/src/marks/rule.js +0 -250
  112. package/src/marks/text.js +0 -278
  113. package/src/node_modules/.vitest/results.json +0 -1
  114. package/src/scale/colorUtils.js +0 -184
  115. package/src/scale/glslScaleGenerator.js +0 -502
  116. package/src/scale/scale.js +0 -451
  117. package/src/scale/scale.test.js +0 -324
  118. package/src/scale/ticks.js +0 -203
  119. package/src/scale/ticks.test.js +0 -40
  120. package/src/singlePageApp.js +0 -13
  121. package/src/spec/axis.d.ts +0 -296
  122. package/src/spec/channel.d.ts +0 -430
  123. package/src/spec/data.d.ts +0 -196
  124. package/src/spec/font.d.ts +0 -15
  125. package/src/spec/genome.d.ts +0 -35
  126. package/src/spec/mark.d.ts +0 -429
  127. package/src/spec/root.d.ts +0 -17
  128. package/src/spec/sampleView.d.ts +0 -180
  129. package/src/spec/scale.d.ts +0 -273
  130. package/src/spec/title.d.ts +0 -102
  131. package/src/spec/tooltip.d.ts +0 -9
  132. package/src/spec/transform.d.ts +0 -479
  133. package/src/spec/view.d.ts +0 -201
  134. package/src/styles/genome-spy.scss +0 -153
  135. package/src/tooltip/dataTooltipHandler.js +0 -64
  136. package/src/tooltip/refseqGeneTooltipHandler.js +0 -78
  137. package/src/tooltip/tooltipHandler.ts +0 -12
  138. package/src/types/filetypes.d.ts +0 -14
  139. package/src/types/flatqueue.d.ts +0 -53
  140. package/src/types/glsl.d.ts +0 -4
  141. package/src/types/internmap.d.ts +0 -22
  142. package/src/types/object.d.ts +0 -21
  143. package/src/types/vega-loader.d.ts +0 -1
  144. package/src/types/vega-scale.d.ts +0 -60
  145. package/src/utils/addBaseUrl.js +0 -19
  146. package/src/utils/addBaseUrl.test.js +0 -22
  147. package/src/utils/animator.js +0 -83
  148. package/src/utils/arrayUtils.js +0 -61
  149. package/src/utils/binnedIndex.js +0 -167
  150. package/src/utils/binnedIndex.test.js +0 -155
  151. package/src/utils/clamp.js +0 -8
  152. package/src/utils/cloner.js +0 -34
  153. package/src/utils/cloner.test.js +0 -24
  154. package/src/utils/coalesce.js +0 -11
  155. package/src/utils/coalesce.test.js +0 -16
  156. package/src/utils/concatIterables.js +0 -26
  157. package/src/utils/concatIterables.test.js +0 -8
  158. package/src/utils/debounce.js +0 -37
  159. package/src/utils/domainArray.js +0 -216
  160. package/src/utils/domainArray.test.js +0 -130
  161. package/src/utils/eerp.js +0 -13
  162. package/src/utils/expression.js +0 -32
  163. package/src/utils/field.js +0 -28
  164. package/src/utils/formatObject.js +0 -31
  165. package/src/utils/indexer.js +0 -43
  166. package/src/utils/indexer.test.js +0 -47
  167. package/src/utils/inertia.js +0 -124
  168. package/src/utils/interactionEvent.js +0 -33
  169. package/src/utils/iterateNestedMaps.js +0 -21
  170. package/src/utils/iterateNestedMaps.test.js +0 -33
  171. package/src/utils/kWayMerge.js +0 -42
  172. package/src/utils/kWayMerge.test.js +0 -26
  173. package/src/utils/layout/flexLayout.js +0 -368
  174. package/src/utils/layout/flexLayout.test.js +0 -311
  175. package/src/utils/layout/grid.js +0 -95
  176. package/src/utils/layout/grid.test.js +0 -71
  177. package/src/utils/layout/padding.js +0 -120
  178. package/src/utils/layout/point.js +0 -23
  179. package/src/utils/layout/rectangle.js +0 -288
  180. package/src/utils/layout/rectangle.test.js +0 -172
  181. package/src/utils/mergeObjects.js +0 -99
  182. package/src/utils/mergeObjects.test.js +0 -42
  183. package/src/utils/numberExtractor.js +0 -24
  184. package/src/utils/numberExtractor.test.js +0 -6
  185. package/src/utils/point.js +0 -14
  186. package/src/utils/propertyCacher.js +0 -70
  187. package/src/utils/propertyCacher.test.js +0 -85
  188. package/src/utils/propertyCoalescer.js +0 -42
  189. package/src/utils/propertyCoalescer.test.js +0 -22
  190. package/src/utils/reservationMap.js +0 -103
  191. package/src/utils/reservationMap.test.js +0 -20
  192. package/src/utils/scaleNull.js +0 -19
  193. package/src/utils/setOperations.js +0 -75
  194. package/src/utils/smoothstep.js +0 -10
  195. package/src/utils/throttle.js +0 -34
  196. package/src/utils/topK.js +0 -76
  197. package/src/utils/topK.test.js +0 -64
  198. package/src/utils/transition.js +0 -74
  199. package/src/utils/ui/tooltip.js +0 -189
  200. package/src/utils/url.js +0 -22
  201. package/src/utils/variableTools.js +0 -24
  202. package/src/utils/variableTools.test.js +0 -13
  203. package/src/view/axisResolution.js +0 -140
  204. package/src/view/axisResolution.test.js +0 -201
  205. package/src/view/axisView.js +0 -747
  206. package/src/view/concatView.js +0 -45
  207. package/src/view/containerView.js +0 -159
  208. package/src/view/facetView.js +0 -491
  209. package/src/view/flowBuilder.js +0 -367
  210. package/src/view/flowBuilder.test.js +0 -125
  211. package/src/view/gridView.js +0 -786
  212. package/src/view/implicitRootView.js +0 -14
  213. package/src/view/importView.js +0 -19
  214. package/src/view/layerView.js +0 -74
  215. package/src/view/rendering.d.ts +0 -44
  216. package/src/view/renderingContext/compositeViewRenderingContext.js +0 -51
  217. package/src/view/renderingContext/deferredViewRenderingContext.js +0 -176
  218. package/src/view/renderingContext/layoutRecorderViewRenderingContext.js +0 -128
  219. package/src/view/renderingContext/simpleViewRenderingContext.js +0 -64
  220. package/src/view/renderingContext/svgViewRenderingContext.js +0 -125
  221. package/src/view/renderingContext/viewRenderingContext.js +0 -41
  222. package/src/view/scaleResolution.js +0 -797
  223. package/src/view/scaleResolution.test.js +0 -572
  224. package/src/view/scaleResolutionApi.d.ts +0 -40
  225. package/src/view/testUtils.js +0 -51
  226. package/src/view/title.js +0 -165
  227. package/src/view/unitView.js +0 -382
  228. package/src/view/view.js +0 -612
  229. package/src/view/view.test.js +0 -214
  230. package/src/view/viewContext.d.ts +0 -62
  231. package/src/view/viewFactory.js +0 -181
  232. package/src/view/viewFactory.test.js +0 -17
  233. package/src/view/viewUtils.js +0 -327
  234. package/src/view/zoom.js +0 -89
@@ -1,199 +0,0 @@
1
- import { isNumber } from "vega-util";
2
- import { ATTRIBUTE_PREFIX } from "../scale/glslScaleGenerator";
3
-
4
- /**
5
- * @typedef {Object} ConverterMetadata
6
- * A function that extracts a raw attribute from a datum (optionally) converts
7
- * it to floats or float vectors that can be stored in GPU buffers.
8
- * @prop {function(object):any} f The converter
9
- * @prop {number[]} [arrayReference] An optimization for fp64 mainly
10
- * @prop {number} [numComponents]
11
- */
12
- export default class ArrayBuilder {
13
- // TODO: Support strided layout. May yield better performance or not. No consensus in literature.
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-
15
- /**
16
- *
17
- * @param {number} size Size if known, uses TypedArray
18
- */
19
- constructor(size) {
20
- this.size = size;
21
-
22
- /** @type {Object.<string, {data: number[] | Float32Array, numComponents: number, divisor?: number}>} */
23
- this.arrays = {};
24
-
25
- /** @type {(function():void)[]} */
26
- this.pushers = [];
27
-
28
- /** @type {(function(any):void)[]} */
29
- this.dataUpdaters = [];
30
-
31
- this.vertexCount = 0;
32
- }
33
-
34
- /**
35
- *
36
- * @param {string} attribute
37
- * @param {ConverterMetadata} metadata
38
- */
39
- addConverter(attribute, metadata) {
40
- const updater = this.createUpdater(
41
- ATTRIBUTE_PREFIX + attribute,
42
- metadata.numComponents || 1,
43
- metadata.arrayReference
44
- );
45
- const f = metadata.f;
46
- this.dataUpdaters.push(
47
- metadata.arrayReference
48
- ? (d) => updater(f(d))
49
- : (d) => updater(f(d))
50
- );
51
- }
52
-
53
- /**
54
- *
55
- * @param {string} attributeName
56
- * @param {number} numComponents
57
- * @param {number[]} [arrayReference]
58
- * @return {function(number|number[])}
59
- */
60
- createUpdater(attributeName, numComponents, arrayReference) {
61
- if (!isNumber(this.size)) {
62
- throw new Error("The number of vertices must be defined!");
63
- }
64
-
65
- /** @type {function():void} */
66
- let pusher;
67
- let updater;
68
- let i = 0;
69
-
70
- const array = new Float32Array(this.size * numComponents);
71
-
72
- this.arrays[attributeName] = {
73
- data: array,
74
- numComponents: numComponents,
75
- };
76
-
77
- if (numComponents == 1) {
78
- let pendingValue = 0;
79
-
80
- /** @param {number} value */
81
- const valueUpdater = (value) => {
82
- pendingValue = +value;
83
- };
84
-
85
- pusher = () => {
86
- array[i++] = pendingValue;
87
- };
88
- updater = valueUpdater;
89
- } else {
90
- let pendingArray = arrayReference ?? [0];
91
-
92
- /** @type {function(number[]):void} value */
93
- const arrayUpdater = arrayReference
94
- ? (value) => {
95
- // Nop. Pending value is updated through the array reference.
96
- }
97
- : (value) => {
98
- pendingArray = value;
99
- };
100
-
101
- switch (numComponents) {
102
- case 1:
103
- break;
104
- case 2:
105
- pusher = () => {
106
- array[i++] = pendingArray[0];
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- array[i++] = pendingArray[1];
108
- };
109
- updater = arrayUpdater;
110
- break;
111
- case 3:
112
- pusher = () => {
113
- array[i++] = pendingArray[0];
114
- array[i++] = pendingArray[1];
115
- array[i++] = pendingArray[2];
116
- };
117
- updater = arrayUpdater;
118
- break;
119
- case 4:
120
- pusher = () => {
121
- array[i++] = pendingArray[0];
122
- array[i++] = pendingArray[1];
123
- array[i++] = pendingArray[2];
124
- array[i++] = pendingArray[3];
125
- };
126
- updater = arrayUpdater;
127
- break;
128
- default:
129
- throw new Error("Invalid numComponents: " + numComponents);
130
- }
131
- }
132
-
133
- this.pushers.push(pusher);
134
-
135
- return updater;
136
- }
137
-
138
- _unrollPushAll() {
139
- let preps = "";
140
- let pushs = "";
141
-
142
- for (let i = 0; i < this.pushers.length; i++) {
143
- preps += `const p${i} = that.pushers[${i}];\n`;
144
- pushs += `p${i}();\n`;
145
- }
146
-
147
- // eslint-disable-next-line no-new-func
148
- const createUnrolled = new Function(
149
- "that",
150
- `${preps}
151
-
152
- return function unrolledPushAll() {
153
- ${pushs}
154
- that.vertexCount++;
155
- };
156
- `
157
- );
158
-
159
- this.pushAll = createUnrolled(this);
160
- }
161
-
162
- pushAll() {
163
- // Unrolling appears to give a 20% performance boost on Chrome but compiling the
164
- // dynamically generated code takes time and is thus not great for small dynamic data.
165
- // Unrolling probably allows the JS engine to inline pusher calls.
166
- const unroll = this.size > 100000;
167
- if (unroll) {
168
- this._unrollPushAll();
169
- } else {
170
- this.pushAll = () => {
171
- for (let i = 0; i < this.pushers.length; i++) {
172
- this.pushers[i]();
173
- }
174
- this.vertexCount++;
175
- };
176
- }
177
-
178
- this.pushAll();
179
- }
180
-
181
- /**
182
- *
183
- * @param {object} datum
184
- */
185
- updateFromDatum(datum) {
186
- for (let i = 0; i < this.dataUpdaters.length; i++) {
187
- this.dataUpdaters[i](datum);
188
- }
189
- }
190
-
191
- /**
192
- *
193
- * @param {object} datum
194
- */
195
- pushFromDatum(datum) {
196
- this.updateFromDatum(datum);
197
- this.pushAll();
198
- }
199
- }